Showing 200 of total 1156 results (show query)
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ComplexHeatmap:Make Complex Heatmaps
Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwarevisualizationsequencingclusteringcomplex-heatmapsheatmap
120.6 match 1.3k stars 16.93 score 16k scripts 151 dependentsbioc
annotate:Annotation for microarrays
Using R enviroments for annotation.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
97.4 match 11.41 score 812 scripts 243 dependentsbioc
annotatr:Annotation of Genomic Regions to Genomic Annotations
Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.
Maintained by Raymond G. Cavalcante. Last updated 5 months ago.
softwareannotationgenomeannotationfunctionalgenomicsvisualizationgenome-annotation
79.3 match 26 stars 9.76 score 246 scripts 5 dependentsmaialba3
LipidMS:Lipid Annotation for LC-MS/MS DDA or DIA Data
Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Maintained by M Isabel Alcoriza-Balaguer. Last updated 7 months ago.
112.4 match 2 stars 5.33 score 12 scripts 1 dependentsbioc
ensembldb:Utilities to create and use Ensembl-based annotation databases
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.
Maintained by Johannes Rainer. Last updated 5 months ago.
geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl
32.7 match 35 stars 14.08 score 892 scripts 108 dependentsbioc
ggtree:an R package for visualization of tree and annotation data
'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.
Maintained by Guangchuang Yu. Last updated 5 months ago.
alignmentannotationclusteringdataimportmultiplesequencealignmentphylogeneticsreproducibleresearchsoftwarevisualizationannotationsggplot2phylogenetic-trees
26.9 match 864 stars 16.86 score 5.1k scripts 109 dependentsbioc
RnBeads:RnBeads
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Maintained by Fabian Mueller. Last updated 1 months ago.
dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport
58.1 match 6.85 score 169 scripts 1 dependentsbioc
genomation:Summary, annotation and visualization of genomic data
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
Maintained by Altuna Akalin. Last updated 5 months ago.
annotationsequencingvisualizationcpgislandcpp
35.7 match 75 stars 11.09 score 738 scripts 5 dependentsropensci
biomartr:Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Maintained by Hajk-Georg Drost. Last updated 1 months ago.
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
34.1 match 218 stars 11.35 score 129 scripts 3 dependentsdfsp-spirit
fsbrain:Managing and Visualizing Brain Surface Data
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Maintained by Tim Schรคfer. Last updated 4 months ago.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
58.3 match 66 stars 6.47 score 15 scriptsbioc
AnnotationDbi:Manipulation of SQLite-based annotations in Bioconductor
Implements a user-friendly interface for querying SQLite-based annotation data packages.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationmicroarraysequencinggenomeannotationbioconductor-packagecore-package
24.8 match 9 stars 15.05 score 3.6k scripts 769 dependentsbioc
OmnipathR:OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Maintained by Denes Turei. Last updated 19 days ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
35.6 match 126 stars 9.90 score 226 scripts 2 dependentsbioc
RCy3:Functions to Access and Control Cytoscape
Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.
Maintained by Alex Pico. Last updated 5 months ago.
visualizationgraphandnetworkthirdpartyclientnetwork
26.3 match 52 stars 13.39 score 628 scripts 15 dependentstidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 9 days ago.
data-visualisationvisualisation
12.9 match 6.6k stars 25.10 score 645k scripts 7.5k dependentskurthornik
NLP:Natural Language Processing Infrastructure
Basic classes and methods for Natural Language Processing.
Maintained by Kurt Hornik. Last updated 4 months ago.
34.3 match 6 stars 9.37 score 1.0k scripts 127 dependentsbioc
biomaRt:Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
Maintained by Mike Smith. Last updated 2 days ago.
annotationbioconductorbiomartensembl
19.6 match 38 stars 15.99 score 13k scripts 230 dependentsbioc
ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationchipseqsoftwarevisualizationmultiplecomparisonatac-seqchip-seqcomparisonepigeneticsepigenomics
23.6 match 234 stars 13.02 score 1.6k scripts 5 dependentsbioc
GenomicFeatures:Query the gene models of a given organism/assembly
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.
Maintained by H. Pagรจs. Last updated 4 months ago.
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
19.9 match 26 stars 15.34 score 5.3k scripts 339 dependentsbioc
BioNAR:Biological Network Analysis in R
the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each proteinโs simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.
Maintained by Anatoly Sorokin. Last updated 19 days ago.
softwaregraphandnetworknetwork
49.7 match 3 stars 5.90 score 35 scriptsdfsp-spirit
freesurferformats:Read and Write 'FreeSurfer' Neuroimaging File Formats
Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Maintained by Tim Schรคfer. Last updated 6 months ago.
brainbrain-atlasbrain-surfacescurvdtifileformatsfreesurferlabelmeshmghmrineuroimagingparcellationresearchsurfacevoxel
35.2 match 23 stars 8.07 score 25 scripts 8 dependentsbioc
MetMashR:Metabolite Mashing with R
A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.
Maintained by Gavin Rhys Lloyd. Last updated 5 months ago.
48.7 match 2 stars 5.81 score 5 scriptsbioc
peakPantheR:Peak Picking and Annotation of High Resolution Experiments
An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.
Maintained by Arnaud Wolfer. Last updated 5 months ago.
massspectrometrymetabolomicspeakdetectionfeature-detectionmass-spectrometry
39.9 match 12 stars 6.82 score 23 scriptsbioc
scDiagnostics:Cell type annotation diagnostics
The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.
Maintained by Anthony Christidis. Last updated 5 months ago.
annotationclassificationclusteringgeneexpressionrnaseqsinglecellsoftwaretranscriptomics
34.4 match 8 stars 7.77 score 46 scriptsbioc
RcisTarget:RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions
RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).
Maintained by Gert Hulselmans. Last updated 5 months ago.
generegulationmotifannotationtranscriptomicstranscriptiongenesetenrichmentgenetarget
26.2 match 37 stars 9.47 score 191 scriptsbioc
txdbmaker:Tools for making TxDb objects from genomic annotations
A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.
Maintained by H. Pagรจs. Last updated 4 months ago.
infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package
25.3 match 3 stars 9.70 score 92 scripts 86 dependentsbioc
SingleR:Reference-Based Single-Cell RNA-Seq Annotation
Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
Maintained by Aaron Lun. Last updated 28 days ago.
softwaresinglecellgeneexpressiontranscriptomicsclassificationclusteringannotationbioconductorsinglercpp
19.0 match 182 stars 12.60 score 2.1k scripts 1 dependentsbnosac
udpipe:Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
This natural language processing toolkit provides language-agnostic 'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency parsing' of raw text. Next to text parsing, the package also allows you to train annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided at <https://universaldependencies.org/format.html>. The techniques are explained in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0 with UDPipe', available at <doi:10.18653/v1/K17-3009>. The toolkit also contains functionalities for commonly used data manipulations on texts which are enriched with the output of the parser. Namely functionalities and algorithms for collocations, token co-occurrence, document term matrix handling, term frequency inverse document frequency calculations, information retrieval metrics (Okapi BM25), handling of multi-word expressions, keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntactical patterns) sentiment scoring and semantic similarity analysis.
Maintained by Jan Wijffels. Last updated 2 years ago.
conlldependency-parserlemmatizationnatural-language-processingnlppos-taggingr-pkgrcpptext-miningtokenizerudpipecpp
20.2 match 215 stars 11.83 score 1.2k scripts 9 dependentsluisdva
annotater:Annotate Package Load Calls
Provides non-invasive annotation of package load calls such as \code{library()}, \code{p_load()}, and \code{require()} so that we can have an idea of what the packages we are loading are meant for.
Maintained by Luis D. Verde Arregoitia. Last updated 5 months ago.
35.0 match 102 stars 6.81 score 21 scriptsbioc
ORFik:Open Reading Frames in Genomics
R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.
Maintained by Haakon Tjeldnes. Last updated 27 days ago.
immunooncologysoftwaresequencingriboseqrnaseqfunctionalgenomicscoveragealignmentdataimportcpp
21.9 match 33 stars 10.63 score 115 scripts 2 dependentsbioc
IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.
geneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicingvisualizationstatisticalmethodtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologytranscriptomicsrnaseqannotationfunctionalpredictiongenepredictiondataimportmultiplecomparisonbatcheffectimmunooncology
23.8 match 108 stars 9.26 score 125 scriptsaphalo
ggpmisc:Miscellaneous Extensions to 'ggplot2'
Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.
Maintained by Pedro J. Aphalo. Last updated 4 months ago.
data-analysisdatavizggplot2-annotationsggplot2-statsstatistics
16.4 match 105 stars 13.32 score 4.4k scripts 14 dependentsbioc
crisprDesign:Comprehensive design of CRISPR gRNAs for nucleases and base editors
Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.
Maintained by Jean-Philippe Fortin. Last updated 11 days ago.
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design
26.4 match 22 stars 8.28 score 80 scripts 3 dependentsstemangiola
tidyHeatmap:A Tidy Implementation of Heatmap
This is a tidy implementation for heatmap. At the moment it is based on the (great) package 'ComplexHeatmap'. The goal of this package is to interface a tidy data frame with this powerful tool. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). Custom grouping of rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...). Labels size adjusted by row and column total number. Default use of Brewer and Viridis palettes.
Maintained by Stefano Mangiola. Last updated 1 months ago.
assaydomaininfrastructurebrewercomplexheatmapcustom-palettedplyrgraphvizheatmapmtcarsplottingrstudioscaletibbletidytidy-data-frametidybulktidyverseviridis
21.3 match 335 stars 10.23 score 197 scripts 1 dependentszhanxw
seqminer:Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R
Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Maintained by Xiaowei Zhan. Last updated 6 months ago.
annotationbcfbgenmeta-analysisnext-generation-sequencingplinksequencingtabixvcfworkflowzlibbzip2libzstdsqlite3cpp
25.9 match 30 stars 8.29 score 111 scripts 6 dependentsbioc
clusterProfiler:A universal enrichment tool for interpreting omics data
This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.
Maintained by Guangchuang Yu. Last updated 4 months ago.
annotationclusteringgenesetenrichmentgokeggmultiplecomparisonpathwaysreactomevisualizationenrichment-analysisgsea
12.5 match 1.1k stars 17.03 score 11k scripts 48 dependentsbioc
AnnotationForge:Tools for building SQLite-based annotation data packages
Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.
Maintained by Bioconductor Package Maintainer. Last updated 3 days ago.
annotationinfrastructurebioconductor-packagecore-package
22.0 match 5 stars 9.62 score 143 scripts 19 dependentsbioc
AnnotationFilter:Facilities for Filtering Bioconductor Annotation Resources
This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationinfrastructuresoftwarebioconductor-packagecore-package
20.5 match 5 stars 10.20 score 45 scripts 162 dependentsbioc
Category:Category Analysis
A collection of tools for performing category (gene set enrichment) analysis.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationgopathwaysgenesetenrichment
26.3 match 7.93 score 183 scripts 16 dependentsedwbaker
sonicscrewdriver:Bioacoustic Analysis and Publication Tools
Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.
Maintained by Ed Baker. Last updated 1 months ago.
28.8 match 6 stars 7.12 score 26 scriptstaxonomicallyinformedannotation
tima:Taxonomically Informed Metabolite Annotation
This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.
Maintained by Adriano Rutz. Last updated 6 days ago.
metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome
30.2 match 9 stars 6.55 score 32 scripts 2 dependentsbioc
categoryCompare:Meta-analysis of high-throughput experiments using feature annotations
Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Maintained by Robert M. Flight. Last updated 5 months ago.
annotationgomultiplecomparisonpathwaysgeneexpressionbioconductor
29.4 match 6 stars 6.68 scorebioc
MSstatsPTM:Statistical Characterization of Post-translational Modifications
MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.
Maintained by Devon Kohler. Last updated 4 months ago.
immunooncologymassspectrometryproteomicssoftwaredifferentialexpressiononechanneltwochannelnormalizationqualitycontrolpost-translational-modificationcpp
24.4 match 10 stars 7.98 score 36 scripts 2 dependentsvalcu
annotator:Image Annotation and Polygon Outlining using Free Drawing
Provides functions to create image annotations through polygon outlining. Annotator has the same function as 'graphics::locator()' but achieves its purpose through drawing, rather than multiple mouse clicks. It is based on the 'htmlwidgets' package and 'fabric.js' JavaScript library <http://fabricjs.com/>.
Maintained by Mihai Valcu. Last updated 1 years ago.
60.9 match 3 stars 3.18 score 4 scriptsbioc
CAMERA:Collection of annotation related methods for mass spectrometry data
Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments
Maintained by Steffen Neumann. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
18.7 match 11 stars 10.27 score 175 scripts 6 dependentsbioc
plotgardener:Coordinate-Based Genomic Visualization Package for R
Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
Maintained by Nicole Kramer. Last updated 5 months ago.
visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhiccpp
18.8 match 308 stars 10.16 score 167 scripts 3 dependentsbioc
recount:Explore and download data from the recount project
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount
19.6 match 41 stars 9.57 score 498 scripts 3 dependentsbioc
GenomicRanges:Representation and manipulation of genomic intervals
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.
Maintained by Hervรฉ Pagรจs. Last updated 4 months ago.
geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package
10.5 match 44 stars 17.75 score 13k scripts 1.3k dependentsbioc
survcomp:Performance Assessment and Comparison for Survival Analysis
Assessment and Comparison for Performance of Risk Prediction (Survival) Models.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressiondifferentialexpressionvisualizationcpp
21.7 match 8.46 score 448 scripts 12 dependentsbioc
CompoundDb:Creating and Using (Chemical) Compound Annotation Databases
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
Maintained by Johannes Rainer. Last updated 2 months ago.
massspectrometrymetabolomicsannotationdatabasesmass-spectrometry
20.9 match 17 stars 8.40 score 69 scripts 1 dependentsobiba
opalr:'Opal' Data Repository Client and 'DataSHIELD' Utils
Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Maintained by Yannick Marcon. Last updated 2 months ago.
22.6 match 3 stars 7.76 score 179 scripts 2 dependentsbioc
VariantAnnotation:Annotation of Genetic Variants
Annotate variants, compute amino acid coding changes, predict coding outcomes.
Maintained by Bioconductor Package Maintainer. Last updated 2 months ago.
dataimportsequencingsnpannotationgeneticsvariantannotationcurlbzip2xz-utilszlib
15.1 match 11.39 score 1.9k scripts 152 dependentsbioc
musicatk:Mutational Signature Comprehensive Analysis Toolkit
Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.
Maintained by Joshua D. Campbell. Last updated 5 months ago.
softwarebiologicalquestionsomaticmutationvariantannotation
24.4 match 13 stars 7.02 score 20 scriptsbioc
rtracklayer:R interface to genome annotation files and the UCSC genome browser
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Maintained by Michael Lawrence. Last updated 8 days ago.
annotationvisualizationdataimportzlibopensslcurl
13.3 match 12.66 score 6.7k scripts 481 dependentsbioc
SummarizedExperiment:A container (S4 class) for matrix-like assays
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Maintained by Hervรฉ Pagรจs. Last updated 5 months ago.
geneticsinfrastructuresequencingannotationcoveragegenomeannotationbioconductor-packagecore-package
10.0 match 34 stars 16.85 score 8.6k scripts 1.2k dependentsbioc
CAGEfightR:Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.
Maintained by Malte Thodberg. Last updated 5 months ago.
softwaretranscriptioncoveragegeneexpressiongeneregulationpeakdetectiondataimportdatarepresentationtranscriptomicssequencingannotationgenomebrowsersnormalizationpreprocessingvisualization
22.5 match 8 stars 7.46 score 67 scripts 1 dependentsbioc
GenomeInfoDb:Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Maintained by Hervรฉ Pagรจs. Last updated 2 months ago.
geneticsdatarepresentationannotationgenomeannotationbioconductor-packagecore-package
10.0 match 32 stars 16.46 score 1.3k scripts 1.7k dependentsbioc
enrichplot:Visualization of Functional Enrichment Result
The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics.
Maintained by Guangchuang Yu. Last updated 2 months ago.
annotationgenesetenrichmentgokeggpathwayssoftwarevisualizationenrichment-analysispathway-analysis
10.0 match 239 stars 15.71 score 3.1k scripts 58 dependentsbioc
DelayedArray:A unified framework for working transparently with on-disk and in-memory array-like datasets
Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, ordinary arrays and, data frames.
Maintained by Hervรฉ Pagรจs. Last updated 1 months ago.
infrastructuredatarepresentationannotationgenomeannotationbioconductor-packagecore-packageu24ca289073
10.0 match 27 stars 15.59 score 538 scripts 1.2k dependentsbioc
hiAnnotator:Functions for annotating GRanges objects
hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.
Maintained by Nirav V Malani. Last updated 5 months ago.
33.1 match 4.65 score 15 scripts 1 dependentsmarce10
warbleR:Streamline Bioacoustic Analysis
Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.
Maintained by Marcelo Araya-Salas. Last updated 2 months ago.
animal-acoustic-signalsaudio-processingbioacousticsspectrogramstreamline-analysiscpp
13.7 match 54 stars 11.01 score 270 scripts 4 dependentsbioc
ViSEAGO:ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.
Maintained by Aurelien Brionne. Last updated 2 months ago.
softwareannotationgogenesetenrichmentmultiplecomparisonclusteringvisualization
22.7 match 6.64 score 22 scriptsbioc
metaMS:MS-based metabolomics annotation pipeline
MS-based metabolomics data processing and compound annotation pipeline.
Maintained by Yann Guitton. Last updated 5 months ago.
immunooncologymassspectrometrymetabolomics
20.1 match 15 stars 7.50 score 15 scriptsbioc
GOexpress:Visualise microarray and RNAseq data using gene ontology annotations
The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.
Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.
softwaregeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentdatarepresentationclusteringtimecoursemicroarraysequencingrnaseqannotationmultiplecomparisonpathwaysgovisualizationimmunooncologybioconductorbioconductor-packagebioconductor-statsgeneontologygeneset-enrichment
22.2 match 9 stars 6.75 score 31 scriptsbioc
DOSE:Disease Ontology Semantic and Enrichment analysis
This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity
10.0 match 119 stars 14.97 score 2.0k scripts 61 dependentsbioc
GOSemSim:GO-terms Semantic Similarity Measures
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
Maintained by Guangchuang Yu. Last updated 5 months ago.
annotationgoclusteringpathwaysnetworksoftwarebioinformaticsgene-ontologysemantic-similaritycpp
10.5 match 63 stars 14.12 score 708 scripts 68 dependentsuscbiostats
aphylo:Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Maintained by George Vega Yon. Last updated 1 years ago.
annotationsinferencephylogeneticsrcpparmadillocpp
26.9 match 6 stars 5.49 score 104 scriptsbioc
genefu:Computation of Gene Expression-Based Signatures in Breast Cancer
This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
Maintained by Benjamin Haibe-Kains. Last updated 4 months ago.
differentialexpressiongeneexpressionvisualizationclusteringclassification
19.8 match 7.42 score 193 scripts 3 dependentsbioc
MetaboAnnotation:Utilities for Annotation of Metabolomics Data
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
Maintained by Johannes Rainer. Last updated 3 months ago.
infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry
20.8 match 15 stars 6.98 score 35 scriptsbioc
Heatplus:Heatmaps with row and/or column covariates and colored clusters
Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.
Maintained by Alexander Ploner. Last updated 5 months ago.
19.1 match 7.63 score 94 scripts 5 dependentsbioc
KEGGREST:Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST is based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationpathwaysthirdpartyclientkeggbioconductor-packagecore-package
10.0 match 9 stars 14.46 score 688 scripts 775 dependentsbioc
gemma.R:A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.
Maintained by Ogan Mancarci. Last updated 4 months ago.
softwaredataimportmicroarraysinglecellthirdpartyclientdifferentialexpressiongeneexpressionbayesianannotationexperimentaldesignnormalizationbatcheffectpreprocessingbioinformaticsgemmagenomicstranscriptomics
19.1 match 10 stars 7.57 score 26 scriptsmelff
memisc:Management of Survey Data and Presentation of Analysis Results
An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.
Maintained by Martin Elff. Last updated 11 days ago.
11.7 match 46 stars 12.34 score 1.2k scripts 13 dependentsbioc
BSgenome:Software infrastructure for efficient representation of full genomes and their SNPs
Infrastructure shared by all the Biostrings-based genome data packages.
Maintained by Hervรฉ Pagรจs. Last updated 2 months ago.
geneticsinfrastructuredatarepresentationsequencematchingannotationsnpbioconductor-packagecore-package
10.0 match 9 stars 14.12 score 1.2k scripts 269 dependentsbioc
psichomics:Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.
Maintained by Nuno Saraiva-Agostinho. Last updated 5 months ago.
sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-toolscpp
20.2 match 36 stars 6.95 score 31 scriptsbioc
hermes:Preprocessing, analyzing, and reporting of RNA-seq data
Provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and 'DESeq2` as well as voom differential expression analyses are available.
Maintained by Daniel Sabanรฉs Bovรฉ. Last updated 5 months ago.
rnaseqdifferentialexpressionnormalizationpreprocessingqualitycontrolrna-seqstatistical-engineering
18.0 match 11 stars 7.77 score 48 scripts 1 dependentsbioc
derfinder:Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
differentialexpressionsequencingrnaseqchipseqdifferentialpeakcallingsoftwareimmunooncologycoverageannotation-agnosticbioconductorderfinder
13.9 match 42 stars 10.03 score 78 scripts 6 dependentsbioc
OrganismDbi:Software to enable the smooth interfacing of different database packages
The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
18.7 match 7.45 score 34 scripts 35 dependentsbioc
gDRcore:Processing functions and interface to process and analyze drug dose-response data
This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.
Maintained by Arkadiusz Gladki. Last updated 4 days ago.
19.0 match 2 stars 7.25 score 4 scripts 1 dependentsmoseleybioinformaticslab
categoryCompare2:Meta-Analysis of High-Throughput Experiments Using Feature Annotations
Facilitates comparison of significant annotations (categories) generated on one or more feature lists. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).
Maintained by Robert M Flight. Last updated 5 months ago.
annotationgomultiplecomparisonpathwaysgeneexpressionbioconductorbioinformaticsgene-annotationgene-expressiongene-sets
55.6 match 1 stars 2.48 score 9 scriptsemmanuelparadis
ape:Analyses of Phylogenetics and Evolution
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Maintained by Emmanuel Paradis. Last updated 10 hours ago.
7.9 match 64 stars 17.22 score 13k scripts 599 dependentsbioc
circRNAprofiler:circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.
Maintained by Simona Aufiero. Last updated 5 months ago.
annotationstructuralpredictionfunctionalpredictiongenepredictiongenomeassemblydifferentialexpression
23.4 match 10 stars 5.78 score 5 scriptsanimint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 27 days ago.
15.2 match 64 stars 8.87 score 173 scriptsstuart-lab
Signac:Analysis of Single-Cell Chromatin Data
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Maintained by Tim Stuart. Last updated 7 months ago.
atacbioinformaticssingle-cellzlibcpp
11.0 match 349 stars 12.19 score 3.7k scripts 1 dependentsbioc
maftools:Summarize, Analyze and Visualize MAF Files
Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.
Maintained by Anand Mayakonda. Last updated 5 months ago.
datarepresentationdnaseqvisualizationdrivermutationvariantannotationfeatureextractionclassificationsomaticmutationsequencingfunctionalgenomicssurvivalbioinformaticscancer-genome-atlascancer-genomicsgenomicsmaf-filestcgacurlbzip2xz-utilszlib
9.1 match 459 stars 14.63 score 948 scripts 18 dependentspyanglab
ClueR:Cluster Evaluation
CLUster Evaluation (CLUE) is a computational method for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms and subsequently identify key kinases or pathways from each cluster. Its implementation in R is called ClueR. See README on <https://github.com/PYangLab/ClueR> for more details. P Yang et al. (2015) <doi:10.1371/journal.pcbi.1004403>.
Maintained by Pengyi Yang. Last updated 1 years ago.
31.5 match 10 stars 4.23 score 17 scriptsbioc
methylKit:DNA methylation analysis from high-throughput bisulfite sequencing results
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
Maintained by Altuna Akalin. Last updated 16 days ago.
dnamethylationsequencingmethylseqgenome-biologymethylationstatistical-analysisvisualizationcurlbzip2xz-utilszlibcpp
11.3 match 220 stars 11.80 score 578 scripts 3 dependentsbioc
HDF5Array:HDF5 datasets as array-like objects in R
The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.
Maintained by Hervรฉ Pagรจs. Last updated 26 days ago.
infrastructuredatarepresentationdataimportsequencingrnaseqcoverageannotationgenomeannotationsinglecellimmunooncologybioconductor-packagecore-packageu24ca289073
10.0 match 12 stars 13.19 score 844 scripts 123 dependentseuropeanifcbgroup
iRfcb:Tools for Managing Imaging FlowCytobot (IFCB) Data
A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learningโclassified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.
Maintained by Anders Torstensson. Last updated 9 hours ago.
22.5 match 1 stars 5.72 scoredavid-barnett
microViz:Microbiome Data Analysis and Visualization
Microbiome data visualization and statistics tools built upon phyloseq.
Maintained by David Barnett. Last updated 3 months ago.
microbiomemicrobiome-analysismicrobiota
20.6 match 114 stars 6.22 score 480 scriptsbioc
cliqueMS:Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerร and M. Sales-Pardo, Bioinformatics, 35(20), 2019), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.
Maintained by Oriol Senan Campos. Last updated 5 months ago.
metabolomicsmassspectrometrynetworknetworkinferencecpp
18.4 match 12 stars 6.91 score 25 scriptsthomasp85
ggforce:Accelerating 'ggplot2'
The aim of 'ggplot2' is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialised plots. 'ggforce' aims to be a collection of mainly new stats and geoms that fills this gap. All additional functionality is aimed to come through the official extension system so using 'ggforce' should be a stable experience.
Maintained by Thomas Lin Pedersen. Last updated 1 years ago.
ggplot-extensionggplot2visualizationcpp
8.0 match 920 stars 15.83 score 9.3k scripts 293 dependentsbioc
ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App
ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.
Maintained by Pacome Prompsy. Last updated 5 months ago.
shinyappssoftwaresinglecellchipseqatacseqmethylseqclassificationclusteringepigeneticsprincipalcomponentannotationbatcheffectmultiplecomparisonnormalizationpathwayspreprocessingqualitycontrolreportwritingvisualizationgenesetenrichmentdifferentialpeakcallingepigenomicsshinysingle-cellcpp
21.7 match 14 stars 5.83 score 16 scriptsbioc
LOLA:Locus overlap analysis for enrichment of genomic ranges
Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.
Maintained by Nathan Sheffield. Last updated 5 months ago.
genesetenrichmentgeneregulationgenomeannotationsystemsbiologyfunctionalgenomicschipseqmethylseqsequencing
13.4 match 76 stars 9.34 score 160 scriptswilkelab
cowplot:Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.
Maintained by Claus O. Wilke. Last updated 2 months ago.
6.6 match 714 stars 18.83 score 75k scripts 1.4k dependentsropensci
treeio:Base Classes and Functions for Phylogenetic Tree Input and Output
'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.
Maintained by Guangchuang Yu. Last updated 5 months ago.
softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees
10.0 match 102 stars 12.46 score 1.3k scripts 122 dependentsbioc
annotationTools:Annotate microarrays and perform cross-species gene expression analyses using flat file databases
Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).
Maintained by Alexandre Kuhn. Last updated 5 months ago.
27.5 match 4.51 score 18 scripts 1 dependentsbioc
ReactomePA:Reactome Pathway Analysis
This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team.
Maintained by Guangchuang Yu. Last updated 5 months ago.
pathwaysvisualizationannotationmultiplecomparisongenesetenrichmentreactomeenrichment-analysisreactome-pathway-analysisreactomepa
10.0 match 40 stars 12.25 score 1.5k scripts 7 dependentsbioc
sitadela:An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
Provides an interface to build a unified database of genomic annotations and their coordinates (gene, transcript and exon levels). It is aimed to be used when simple tab-delimited annotations (or simple GRanges objects) are required instead of the more complex annotation Bioconductor packages. Also useful when combinatorial annotation elements are reuired, such as RefSeq coordinates with Ensembl biotypes. Finally, it can download, construct and handle annotations with versioned genes and transcripts (where available, e.g. RefSeq and latest Ensembl). This is particularly useful in precision medicine applications where the latter must be reported.
Maintained by Panagiotis Moulos. Last updated 5 months ago.
softwareworkflowsteprnaseqtranscriptionsequencingtranscriptomicsbiomedicalinformaticsfunctionalgenomicssystemsbiologyalternativesplicingdataimportchipseq
26.6 match 4.60 score 2 scriptstomkellygenetics
vioplot:Violin Plot
A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Maintained by S. Thomas Kelly. Last updated 21 days ago.
boxplotcolourscustomisationdatavizformulaplottingviolin-plotviolinplotvioplot
9.8 match 26 stars 12.32 score 2.0k scripts 8 dependentspascalcroteau
matrixset:Creating, Manipulating and Annotating Matrix Ensemble
Creates an object that stores a matrix ensemble, matrices that share the same common properties, where rows and columns can be annotated. Matrices must have the same dimension and dimnames. Operators to manipulate these objects are provided as well as mechanisms to apply functions to these objects.
Maintained by Pascal Croteau. Last updated 2 months ago.
23.6 match 2 stars 5.12 score 11 scriptsbioc
Biobase:Biobase: Base functions for Bioconductor
Functions that are needed by many other packages or which replace R functions.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
infrastructurebioconductor-packagecore-package
7.3 match 9 stars 16.45 score 6.6k scripts 1.8k dependentsbioc
geneXtendeR:Optimized Functional Annotation Of ChIP-seq Data
geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.
Maintained by Bohdan Khomtchouk. Last updated 5 months ago.
chipseqgeneticsannotationgenomeannotationdifferentialpeakcallingcoveragepeakdetectionchiponchiphistonemodificationdataimportnaturallanguageprocessingvisualizationgosoftwarebioconductorbioinformaticscchip-seqcomputational-biologyepigeneticsfunctional-annotation
30.2 match 9 stars 3.95 score 5 scriptsbioc
minfi:Analyze Illumina Infinium DNA methylation arrays
Tools to analyze & visualize Illumina Infinium methylation arrays.
Maintained by Kasper Daniel Hansen. Last updated 4 months ago.
immunooncologydnamethylationdifferentialmethylationepigeneticsmicroarraymethylationarraymultichanneltwochanneldataimportnormalizationpreprocessingqualitycontrol
9.3 match 60 stars 12.83 score 996 scripts 26 dependentsbioc
metaseqR2:An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.
Maintained by Panagiotis Moulos. Last updated 5 days ago.
softwaregeneexpressiondifferentialexpressionworkflowsteppreprocessingqualitycontrolnormalizationreportwritingrnaseqtranscriptionsequencingtranscriptomicsbayesianclusteringcellbiologybiomedicalinformaticsfunctionalgenomicssystemsbiologyimmunooncologyalternativesplicingdifferentialsplicingmultiplecomparisontimecoursedataimportatacseqepigeneticsregressionproprietaryplatformsgenesetenrichmentbatcheffectchipseq
19.5 match 7 stars 6.05 score 3 scriptsbioc
annaffy:Annotation tools for Affymetrix biological metadata
Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.
Maintained by Colin A. Smith. Last updated 5 months ago.
onechannelmicroarrayannotationgopathwaysreportwriting
20.9 match 5.64 score 60 scripts 3 dependentsbioc
proActiv:Estimate Promoter Activity from RNA-Seq data
Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.
Maintained by Joseph Lee. Last updated 5 months ago.
rnaseqgeneexpressiontranscriptionalternativesplicinggeneregulationdifferentialsplicingfunctionalgenomicsepigeneticstranscriptomicspreprocessingalternative-promotersgenomicspromoter-activitypromoter-annotationrna-seq-data
17.6 match 51 stars 6.66 score 15 scriptsbioc
cola:A Framework for Consensus Partitioning
Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.
Maintained by Zuguang Gu. Last updated 1 months ago.
clusteringgeneexpressionclassificationsoftwareconsensus-clusteringcpp
15.5 match 61 stars 7.49 score 112 scriptsbioc
simona:Semantic Similarity on Bio-Ontologies
This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.
Maintained by Zuguang Gu. Last updated 5 months ago.
softwareannotationgobiomedicalinformaticscpp
17.5 match 16 stars 6.59 score 27 scripts 1 dependentsbioc
recount3:Explore and download data from the recount3 project
The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3
14.3 match 33 stars 8.03 score 216 scriptsbioc
GenomicInteractions:Utilities for handling genomic interaction data
Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.
Maintained by Liz Ing-Simmons. Last updated 5 months ago.
softwareinfrastructuredataimportdatarepresentationhic
12.1 match 7 stars 9.39 score 162 scripts 6 dependentsbioc
BiocGenerics:S4 generic functions used in Bioconductor
The package defines many S4 generic functions used in Bioconductor.
Maintained by Hervรฉ Pagรจs. Last updated 1 months ago.
infrastructurebioconductor-packagecore-package
8.0 match 12 stars 14.22 score 612 scripts 2.2k dependentsaphalo
ggpp:Grammar Extensions to 'ggplot2'
Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve; combined stacking and nudging; combined dodging and nudging.
Maintained by Pedro J. Aphalo. Last updated 21 days ago.
data-labelsdatavizggplot2-enhancementsggplot2-geomsggplot2-insetsggplot2-positions
9.1 match 130 stars 12.49 score 582 scripts 24 dependentsbioc
PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Maintained by Benjamin Haibe-Kains. Last updated 2 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp
9.9 match 68 stars 11.39 score 442 scripts 3 dependentsbioc
beadarray:Quality assessment and low-level analysis for Illumina BeadArray data
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Maintained by Mark Dunning. Last updated 5 months ago.
microarrayonechannelqualitycontrolpreprocessing
14.0 match 7.88 score 70 scripts 4 dependentsdavidgohel
ggiraph:Make 'ggplot2' Graphics Interactive
Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Maintained by David Gohel. Last updated 3 months ago.
7.5 match 819 stars 14.39 score 4.1k scripts 34 dependentsbioc
GenomicScores:Infrastructure to work with genomewide position-specific scores
Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.
Maintained by Robert Castelo. Last updated 1 months ago.
infrastructuregeneticsannotationsequencingcoverageannotationhubsoftware
12.4 match 8 stars 8.71 score 83 scripts 6 dependentsbioc
ggmsa:Plot Multiple Sequence Alignment using 'ggplot2'
A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.
Maintained by Guangchuang Yu. Last updated 3 months ago.
softwarevisualizationalignmentannotationmultiplesequencealignment
11.5 match 209 stars 9.34 score 196 scripts 2 dependentsrickhelmus
patRoon:Workflows for Mass-Spectrometry Based Non-Target Analysis
Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.
Maintained by Rick Helmus. Last updated 10 days ago.
mass-spectrometrynon-targetcppopenjdk
17.3 match 65 stars 6.22 score 43 scriptsbioc
tximeta:Transcript Quantification Import with Automatic Metadata
Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.
Maintained by Michael Love. Last updated 2 months ago.
annotationgenomeannotationdataimportpreprocessingrnaseqsinglecelltranscriptomicstranscriptiongeneexpressionfunctionalgenomicsreproducibleresearchreportwritingimmunooncology
10.0 match 67 stars 10.58 score 466 scripts 1 dependentsbioc
OmaDB:R wrapper for the OMA REST API
A package for the orthology prediction data download from OMA database.
Maintained by Klara Kaleb. Last updated 5 months ago.
softwarecomparativegenomicsfunctionalgenomicsgeneticsannotationgofunctionalprediction
17.0 match 2 stars 6.23 score 5 scriptsbioc
SWATH2stats:Transform and Filter SWATH Data for Statistical Packages
This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.
Maintained by Peter Blattmann. Last updated 5 months ago.
proteomicsannotationexperimentaldesignpreprocessingmassspectrometryimmunooncology
16.8 match 1 stars 6.30 score 22 scriptsbioc
NetPathMiner:NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.
Maintained by Ahmed Mohamed. Last updated 4 months ago.
graphandnetworkpathwaysnetworkclusteringclassificationlibsbmllibxml2openblascpp
16.1 match 9 stars 6.56 score 9 scriptsbioc
scRepertoire:A toolkit for single-cell immune receptor profiling
scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.
Maintained by Nick Borcherding. Last updated 2 months ago.
softwareimmunooncologysinglecellclassificationannotationsequencingcpp
10.0 match 326 stars 10.49 score 240 scriptsbioc
customCMPdb:Customize and Query Compound Annotation Database
This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.
Maintained by Yuzhu Duan. Last updated 5 months ago.
softwarecheminformaticsannotationhubsoftware
21.5 match 2 stars 4.78 score 4 scriptsbioc
BiocIO:Standard Input and Output for Bioconductor Packages
The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.
Maintained by Marcel Ramos. Last updated 4 months ago.
annotationdataimportbioconductor-packagecore-package
10.0 match 1 stars 10.20 score 19 scripts 487 dependentsbioc
SGSeq:Splice event prediction and quantification from RNA-seq data
SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.
Maintained by Leonard Goldstein. Last updated 5 months ago.
alternativesplicingimmunooncologyrnaseqtranscription
17.1 match 5.91 score 45 scripts 3 dependentsbioc
atena:Analysis of Transposable Elements
Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.
Maintained by Robert Castelo. Last updated 1 months ago.
transcriptiontranscriptomicsrnaseqsequencingpreprocessingsoftwaregeneexpressioncoveragedifferentialexpressionfunctionalgenomics
16.4 match 10 stars 6.18 score 1 scriptsbioc
UCSC.utils:Low-level utilities to retrieve data from the UCSC Genome Browser
A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.
Maintained by Hervรฉ Pagรจs. Last updated 2 months ago.
infrastructuregenomeassemblyannotationgenomeannotationdataimportbioconductor-packagecore-package
10.0 match 1 stars 10.09 score 4 scripts 1.7k dependentsbioc
CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters
This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.
Maintained by Michael Shapiro. Last updated 1 months ago.
biologicalquestionstatisticalmethodgeneexpressionsinglecelltranscriptomicsspatial
15.4 match 3 stars 6.50 scorebioc
csaw:ChIP-Seq Analysis with Windows
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Maintained by Aaron Lun. Last updated 2 months ago.
multiplecomparisonchipseqnormalizationsequencingcoveragegeneticsannotationdifferentialpeakcallingcurlbzip2xz-utilszlibcpp
12.0 match 8.32 score 498 scripts 7 dependentspyanglab
directPA:Direction Analysis for Pathways and Kinases
Direction analysis is a set of tools designed to identify combinatorial effects of multiple treatments/conditions on pathways and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.
Maintained by Pengyi Yang. Last updated 1 years ago.
24.0 match 4.14 score 31 scripts 1 dependentssistm
cytometree:Automated Cytometry Gating and Annotation
Given the hypothesis of a bi-modal distribution of cells for each marker, the algorithm constructs a binary tree, the nodes of which are subpopulations of cells. At each node, observed cells and markers are modeled by both a family of normal distributions and a family of bi-modal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families. Method is detailed in: Commenges, Alkhassim, Gottardo, Hejblum & Thiebaut (2018) <doi: 10.1002/cyto.a.23601>.
Maintained by Boris P Hejblum. Last updated 2 years ago.
16.8 match 9 stars 5.91 score 15 scripts 1 dependentsbioc
MSstatsShiny:MSstats GUI for Statistical Anaylsis of Proteomics Experiments
MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.
Maintained by Devon Kohler. Last updated 5 months ago.
immunooncologymassspectrometryproteomicssoftwareshinyappsdifferentialexpressiononechanneltwochannelnormalizationqualitycontrolgui
15.3 match 15 stars 6.43 score 4 scriptsbioc
ggtreeExtra:An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.
Maintained by Shuangbin Xu. Last updated 5 months ago.
softwarevisualizationphylogeneticsannotation
10.0 match 90 stars 9.72 score 426 scripts 3 dependentsoliverehmer
act:Aligned Corpus Toolkit
The Aligned Corpus Toolkit (act) is designed for linguists that work with time aligned transcription data. It offers functions to import and export various annotation file formats ('ELAN' .eaf, 'EXMARaLDA .exb and 'Praat' .TextGrid files), create print transcripts in the style of conversation analysis, search transcripts (span searches across multiple annotations, search in normalized annotations, make concordances etc.), export and re-import search results (.csv and 'Excel' .xlsx format), create cuts for the search results (print transcripts, audio/video cuts using 'FFmpeg' and video sub titles in 'Subrib title' .srt format), modify the data in a corpus (search/replace, delete, filter etc.), interact with 'Praat' using 'Praat'-scripts, and exchange data with the 'rPraat' package. The package is itself written in R and may be expanded by other users.
Maintained by Oliver Ehmer. Last updated 2 years ago.
14.6 match 4 stars 6.65 score 184 scriptsbioc
scp:Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.
Maintained by Christophe Vanderaa. Last updated 16 days ago.
geneexpressionproteomicssinglecellmassspectrometrypreprocessingcellbasedassaysbioconductormass-spectrometrysingle-cellsoftware
10.9 match 25 stars 8.94 score 115 scriptsbioc
goseq:Gene Ontology analyser for RNA-seq and other length biased data
Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.
Maintained by Federico Marini. Last updated 5 months ago.
immunooncologysequencinggogeneexpressiontranscriptionrnaseqdifferentialexpressionannotationgenesetenrichmentkeggpathwayssoftware
10.0 match 1 stars 9.67 score 636 scripts 9 dependentsbioc
SCANVIS:SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
SCANVIS is a set of annotation-dependent tools for analyzing splice junctions and their read support as predetermined by an alignment tool of choice (for example, STAR aligner). SCANVIS assesses each junction's relative read support (RRS) by relating to the context of local split reads aligning to annotated transcripts. SCANVIS also annotates each splice junction by indicating whether the junction is supported by annotation or not, and if not, what type of junction it is (e.g. exon skipping, alternative 5' or 3' events, Novel Exons). Unannotated junctions are also futher annotated by indicating whether it induces a frame shift or not. SCANVIS includes a visualization function to generate static sashimi-style plots depicting relative read support and number of split reads using arc thickness and arc heights, making it easy for users to spot well-supported junctions. These plots also clearly delineate unannotated junctions from annotated ones using designated color schemes, and users can also highlight splice junctions of choice. Variants and/or a read profile are also incoroporated into the plot if the user supplies variants in bed format and/or the BAM file. One further feature of the visualization function is that users can submit multiple samples of a certain disease or cohort to generate a single plot - this occurs via a "merge" function wherein junction details over multiple samples are merged to generate a single sashimi plot, which is useful when contrasting cohorots (eg. disease vs control).
Maintained by Phaedra Agius. Last updated 5 months ago.
softwareresearchfieldtranscriptomicsworkflowstepannotationvisualization
24.1 match 4.00 score 2 scriptsbioc
clustifyr:Classifier for Single-cell RNA-seq Using Cell Clusters
Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.
Maintained by Rui Fu. Last updated 5 months ago.
singlecellannotationsequencingmicroarraygeneexpressionassign-identitiesclustersmarker-genesrna-seqsingle-cell-rna-seq
10.0 match 119 stars 9.63 score 296 scriptsbioc
raer:RNA editing tools in R
Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.
Maintained by Kent Riemondy. Last updated 5 months ago.
multiplecomparisonrnaseqsinglecellsequencingcoverageepitranscriptomicsfeatureextractionannotationalignmentbioconductor-packagerna-seq-analysissingle-cell-analysissingle-cell-rna-seqcurlbzip2xz-utilszlib
15.9 match 8 stars 5.98 score 6 scriptsbioc
StructuralVariantAnnotation:Variant annotations for structural variants
StructuralVariantAnnotation provides a framework for analysis of structural variants within the Bioconductor ecosystem. This package contains contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.
Maintained by Daniel Cameron. Last updated 5 months ago.
dataimportsequencingannotationgeneticsvariantannotation
15.0 match 6.26 score 102 scripts 2 dependentsbioc
Gviz:Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
Maintained by Robert Ivanek. Last updated 5 months ago.
visualizationmicroarraysequencing
7.1 match 79 stars 13.08 score 1.4k scripts 48 dependentsbioc
Organism.dplyr:dplyr-based Access to Bioconductor Annotation Resources
This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).
Maintained by Martin Morgan. Last updated 5 months ago.
annotationsequencinggenomeannotationbioconductor-packagecore-package
13.4 match 3 stars 6.77 score 63 scripts 1 dependentsbioc
BgeeDB:Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.
Maintained by Julien Wollbrett. Last updated 5 months ago.
softwaredataimportsequencinggeneexpressionmicroarraygogenesetenrichmentbioinformaticsenrichment-analysisrna-seqscrna-seqsingle-cell
10.7 match 15 stars 8.46 score 19 scripts 1 dependentsbioc
GOstats:Tools for manipulating GO and microarrays
A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
annotationgomultiplecomparisongeneexpressionmicroarraypathwaysgenesetenrichmentgraphandnetwork
13.0 match 6.93 score 528 scripts 12 dependentsbioc
AlphaMissenseR:Accessing AlphaMissense Data Resources in R
The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.
Maintained by Martin Morgan. Last updated 5 months ago.
snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology
13.1 match 8 stars 6.86 score 10 scriptszjufanlab
scCATCH:Single Cell Cluster-Based Annotation Toolkit for Cellular Heterogeneity
An automatic cluster-based annotation pipeline based on evidence-based score by matching the marker genes with known cell markers in tissue-specific cell taxonomy reference database for single-cell RNA-seq data. See Shao X, et al (2020) <doi:10.1016/j.isci.2020.100882> for more details.
Maintained by Xin Shao. Last updated 2 years ago.
cell-markerscluster-annotationmarker-genesrna-seqsequencingseuratsingle-celltranscriptometranscriptomics
12.6 match 225 stars 7.13 score 75 scriptsbioc
mygene:Access MyGene.Info_ services
MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.
Maintained by Adam Mark, Cyrus Afrasiabi, Chunlei Wu. Last updated 5 months ago.
12.3 match 7.17 score 330 scripts 1 dependentsbioc
UniProt.ws:R Interface to UniProt Web Services
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. This package provides a collection of functions for retrieving, processing, and re-packaging UniProt web services. The package makes use of UniProt's modernized REST API and allows mapping of identifiers accross different databases.
Maintained by Marcel Ramos. Last updated 2 months ago.
annotationinfrastructuregokeggbiocartabioconductor-packagecore-package
10.5 match 4 stars 8.38 score 167 scripts 4 dependentsms609
Ternary:Create Ternary and Holdridge Plots
Plots ternary diagrams (simplex plots / Gibbs triangles) and Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the standard graphics functions. Allows custom annotation, interpolating, contouring and scaling of plotting region. Includes a 'Shiny' user interface for point-and-click ternary plotting. An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Maintained by Martin R. Smith. Last updated 5 months ago.
graphicsplottingplotting-in-rternary-plots
9.1 match 33 stars 9.58 score 103 scripts 5 dependentsbioc
cellbaseR:Querying annotation data from the high performance Cellbase web
This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.
Maintained by Mohammed OE Abdallah. Last updated 5 months ago.
16.0 match 2 stars 5.48 score 6 scriptsbioc
cogeqc:Systematic quality checks on comparative genomics analyses
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.
Maintained by Fabrรญcio Almeida-Silva. Last updated 5 months ago.
softwaregenomeassemblycomparativegenomicsfunctionalgenomicsphylogeneticsqualitycontrolnetworkcomparative-genomicsevolutionary-genomics
14.2 match 10 stars 6.08 score 20 scriptsbioc
EnrichDO:a Global Weighted Model for Disease Ontology Enrichment Analysis
To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data.
Maintained by Hongyu Fu. Last updated 4 months ago.
annotationvisualizationgenesetenrichmentsoftware
18.1 match 4.74 score 9 scriptsjbgruber
rollama:Communicate with 'Ollama' to Run Large Language Models Locally
Wraps the 'Ollama' <https://ollama.com> API, which can be used to communicate with generative large language models locally.
Maintained by Johannes B. Gruber. Last updated 1 months ago.
10.3 match 110 stars 8.36 score 52 scriptsncss-tech
aqp:Algorithms for Quantitative Pedology
The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Maintained by Dylan Beaudette. Last updated 29 days ago.
digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda
7.3 match 55 stars 11.77 score 1.2k scripts 2 dependentsbioc
fobitools:Tools for Manipulating the FOBI Ontology
A set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.
Maintained by Pol Castellano-Escuder. Last updated 4 months ago.
massspectrometrymetabolomicssoftwarevisualizationbiomedicalinformaticsgraphandnetworkannotationcheminformaticspathwaysgenesetenrichmentbiological-intrerpretationbiological-knowledgebiological-significance-analysisenrichment-analysisfood-biomarker-ontologyknowledge-graphnutritionobofoundryontologytext-mining
16.8 match 1 stars 5.08 score 5 scriptsbioc
RMassBank:Workflow to process tandem MS files and build MassBank records
Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Maintained by RMassBank at Eawag. Last updated 5 months ago.
immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk
13.7 match 6.19 score 26 scriptsplangfelder
WGCNA:Weighted Correlation Network Analysis
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Maintained by Peter Langfelder. Last updated 6 months ago.
8.8 match 54 stars 9.65 score 5.3k scripts 32 dependentshrbrmstr
ggalt:Extra Coordinate Systems, 'Geoms', Statistical Transformations, Scales and Fonts for 'ggplot2'
A compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for 'ggplot2', including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the 'PROJ.4'-library along with geom_cartogram() that mimics the original functionality of geom_map(), formatters for "bytes", a stat_stepribbon() function, increased 'plotly' compatibility and the 'StateFace' open source font 'ProPublica'. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.
Maintained by Bob Rudis. Last updated 2 years ago.
geomggplot-extensionggplot2ggplot2-geomggplot2-scales
6.6 match 674 stars 12.59 score 2.3k scripts 7 dependentsmpierrejean
acnr:Annotated Copy-Number Regions
This data package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.
Maintained by Morgane Pierre-Jean. Last updated 3 years ago.
15.9 match 1 stars 5.23 score 19 scripts 3 dependentsbioc
rols:An R interface to the Ontology Lookup Service
The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.
Maintained by Laurent Gatto. Last updated 5 months ago.
immunooncologysoftwareannotationmassspectrometrygo
10.0 match 11 stars 8.30 score 89 scripts 5 dependentsbioc
NanoMethViz:Visualise methylation data from Oxford Nanopore sequencing
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
Maintained by Shian Su. Last updated 7 days ago.
softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp
11.9 match 26 stars 6.95 score 11 scriptsbioc
GeneTonic:Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.
Maintained by Federico Marini. Last updated 2 months ago.
guigeneexpressionsoftwaretranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysreportwritinggenesetenrichmentannotationgoshinyappsbioconductorbioconductor-packagedata-explorationdata-visualizationfunctional-enrichment-analysisgene-expressionpathway-analysisreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly
10.0 match 77 stars 8.28 score 37 scripts 1 dependentsusepa
tcpl:ToxCast Data Analysis Pipeline
The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
Maintained by Jason Brown. Last updated 3 days ago.
8.8 match 36 stars 9.41 score 90 scriptsbioboot
bio3d:Biological Structure Analysis
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintained by Barry Grant. Last updated 5 months ago.
9.8 match 5 stars 8.49 score 1.4k scripts 10 dependentsbioc
hypeR:An R Package For Geneset Enrichment Workflows
An R Package for Geneset Enrichment Workflows.
Maintained by Anthony Federico. Last updated 5 months ago.
genesetenrichmentannotationpathwaysbioinformaticscomputational-biologygeneset-enrichment-analysis
10.0 match 76 stars 8.22 score 145 scriptsthe-hull
datacleanr:Interactive and Reproducible Data Cleaning
Flexible and efficient cleaning of data with interactivity. 'datacleanr' facilitates best practices in data analyses and reproducibility with built-in features and by translating interactive/manual operations to code. The package is designed for interoperability, and so seamlessly fits into reproducible analyses pipelines in 'R'.
Maintained by Alexander Hurley. Last updated 3 years ago.
annotation-tooldata-cleaningoutlier-detectionoutlier-removalreproducibility
18.8 match 20 stars 4.38 score 24 scriptsbioc
CNEr:CNE Detection and Visualization
Large-scale identification and advanced visualization of sets of conserved noncoding elements.
Maintained by Ge Tan. Last updated 5 months ago.
generegulationvisualizationdataimport
8.8 match 3 stars 9.28 score 35 scripts 19 dependentsbioc
PREDA:Position Related Data Analysis
Package for the position related analysis of quantitative functional genomics data.
Maintained by Francesco Ferrari. Last updated 5 months ago.
softwarecopynumbervariationgeneexpressiongenetics
19.1 match 4.30 score 9 scriptsbioc
PhosR:A set of methods and tools for comprehensive analysis of phosphoproteomics data
PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.
Maintained by Taiyun Kim. Last updated 5 months ago.
softwareresearchfieldproteomics
17.4 match 4.71 score 51 scriptsbioc
artMS:Analytical R tools for Mass Spectrometry
artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.
Maintained by David Jimenez-Morales. Last updated 5 months ago.
proteomicsdifferentialexpressionbiomedicalinformaticssystemsbiologymassspectrometryannotationqualitycontrolgenesetenrichmentclusteringnormalizationimmunooncologymultiplecomparisonanalysisanalyticalap-msbioconductorbioinformaticsmass-spectrometryphosphoproteomicspost-translational-modificationquantitative-analysis
12.8 match 14 stars 6.41 score 13 scriptsbioc
nullranges:Generation of null ranges via bootstrapping or covariate matching
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.
Maintained by Michael Love. Last updated 5 months ago.
visualizationgenesetenrichmentfunctionalgenomicsepigeneticsgeneregulationgenetargetgenomeannotationannotationgenomewideassociationhistonemodificationchipseqatacseqdnaseseqrnaseqhiddenmarkovmodelbioconductorbootstrapgenomicsmatchingstatistics
10.0 match 27 stars 8.16 score 50 scripts 1 dependentsbioc
Rsubread:Mapping, quantification and variant analysis of sequencing data
Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.
Maintained by Wei Shi. Last updated 2 days ago.
sequencingalignmentsequencematchingrnaseqchipseqsinglecellgeneexpressiongeneregulationgeneticsimmunooncologysnpgeneticvariabilitypreprocessingqualitycontrolgenomeannotationgenefusiondetectionindeldetectionvariantannotationvariantdetectionmultiplesequencealignmentzlib
8.8 match 9.24 score 892 scripts 10 dependentsr-forge
genoPlotR:Plot Publication-Grade Gene and Genome Maps
Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.
Maintained by Lionel Guy. Last updated 4 years ago.
15.1 match 5.33 score 106 scriptsbioc
BUSpaRse:kallisto | bustools R utilities
The kallisto | bustools pipeline is a fast and modular set of tools to convert single cell RNA-seq reads in fastq files into gene count or transcript compatibility counts (TCC) matrices for downstream analysis. Central to this pipeline is the barcode, UMI, and set (BUS) file format. This package serves the following purposes: First, this package allows users to manipulate BUS format files as data frames in R and then convert them into gene count or TCC matrices. Furthermore, since R and Rcpp code is easier to handle than pure C++ code, users are encouraged to tweak the source code of this package to experiment with new uses of BUS format and different ways to convert the BUS file into gene count matrix. Second, this package can conveniently generate files required to generate gene count matrices for spliced and unspliced transcripts for RNA velocity. Here biotypes can be filtered and scaffolds and haplotypes can be removed, and the filtered transcriptome can be extracted and written to disk. Third, this package implements utility functions to get transcripts and associated genes required to convert BUS files to gene count matrices, to write the transcript to gene information in the format required by bustools, and to read output of bustools into R as sparses matrices.
Maintained by Lambda Moses. Last updated 5 months ago.
singlecellrnaseqworkflowstepcpp
10.9 match 9 stars 7.35 score 165 scriptsbioc
Qtlizer:Comprehensive QTL annotation of GWAS results
This R package provides access to the Qtlizer web server. Qtlizer annotates lists of common small variants (mainly SNPs) and genes in humans with associated changes in gene expression using the most comprehensive database of published quantitative trait loci (QTLs).
Maintained by Matthias Munz. Last updated 16 days ago.
genomewideassociationsnpgeneticslinkagedisequilibriumeqtlgwasvariant-annotation
13.9 match 3 stars 5.73 score 2 scriptssergeitarasov
ontoFAST:Interactive Annotation of Characters with Biological Ontologies
Tools for annotating characters (character matrices) with anatomical and phenotype ontologies. Includes functions for visualising character annotations and creating simple queries using ontological relationships.
Maintained by Sergei Tarasov. Last updated 3 years ago.
annotationscharacter-matricescharactersontologyphylogenetics
26.5 match 2 stars 3.00 score 5 scriptsbioc
packFinder:de novo Annotation of Pack-TYPE Transposable Elements
Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).
Maintained by Jack Gisby. Last updated 5 months ago.
geneticssequencematchingannotationbioinformaticstext-mining
16.4 match 7 stars 4.85 score 6 scriptscox-labs
PerseusR:Perseus R Interop
Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.
Maintained by Jan Rudolph. Last updated 3 years ago.
bioinformaticsinteropmaxquantperseusproteomics
13.5 match 13 stars 5.88 score 58 scriptsclewerenz
ilabelled:Simple Handling of Labelled Data
Simple handling of survey data. Smart handling of meta-information like e.g. variable-labels value-labels and scale-levels. Easy access and validation of meta-information. Useage of value labels and values respectively for subsetting and recoding data.
Maintained by Christof Lewerenz. Last updated 2 months ago.
13.0 match 2 stars 6.02 score 13 scriptsbioc
recoup:An R package for the creation of complex genomic profile plots
recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.
Maintained by Panagiotis Moulos. Last updated 5 months ago.
immunooncologysoftwaregeneexpressionpreprocessingqualitycontrolrnaseqchipseqsequencingcoverageatacseqchiponchipalignmentdataimport
15.5 match 1 stars 5.02 score 2 scriptsbioc
rrvgo:Reduce + Visualize GO
Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity.
Maintained by Sergi Sayols. Last updated 5 months ago.
annotationclusteringgonetworkpathwayssoftware
10.0 match 24 stars 7.74 score 190 scriptskasperwelbers
corpustools:Managing, Querying and Analyzing Tokenized Text
Provides text analysis in R, focusing on the use of a tokenized text format. In this format, the positions of tokens are maintained, and each token can be annotated (e.g., part-of-speech tags, dependency relations). Prominent features include advanced Lucene-like querying for specific tokens or contexts (e.g., documents, sentences), similarity statistics for words and documents, exporting to DTM for compatibility with many text analysis packages, and the possibility to reconstruct original text from tokens to facilitate interpretation.
Maintained by Kasper Welbers. Last updated 6 months ago.
10.3 match 31 stars 7.50 score 174 scripts 1 dependentsbioc
crisprViz:Visualization Functions for CRISPR gRNAs
Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.
Maintained by Jean-Philippe Fortin. Last updated 5 months ago.
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-analysiscrispr-designgrnagrna-sequencegrna-sequencessgrnasgrna-designvisualization
12.3 match 7 stars 6.23 score 6 scripts 2 dependentsbioc
mgsa:Model-based gene set analysis
Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.
Maintained by Sebastian Bauer. Last updated 5 months ago.
pathwaysgogenesetenrichmentopenmp
12.6 match 5 stars 6.08 score 12 scriptsmatrix-profile-foundation
tsmp:Time Series with Matrix Profile
A toolkit implementing the Matrix Profile concept that was created by CS-UCR <http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Maintained by Francisco Bischoff. Last updated 3 years ago.
algorithmmatrix-profilemotif-searchtime-seriescpp
10.4 match 72 stars 7.29 score 179 scripts 1 dependentspolmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
9.5 match 49 stars 7.96 score 311 scriptsbioc
meshr:Tools for conducting enrichment analysis of MeSH
A set of annotation maps describing the entire MeSH assembled using data from MeSH.
Maintained by Koki Tsuyuzaki. Last updated 5 months ago.
annotationdatafunctionalannotationbioinformaticsstatisticsannotationmultiplecomparisonsmeshdb
16.6 match 4.56 score 9 scripts 1 dependentsbioc
pathview:a tool set for pathway based data integration and visualization
Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
Maintained by Weijun Luo. Last updated 5 months ago.
pathwaysgraphandnetworkvisualizationgenesetenrichmentdifferentialexpressiongeneexpressionmicroarrayrnaseqgeneticsmetabolomicsproteomicssystemsbiologysequencing
6.7 match 40 stars 11.24 score 1.6k scripts 10 dependentsbioc
maser:Mapping Alternative Splicing Events to pRoteins
This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.
Maintained by Diogo F.T. Veiga. Last updated 5 months ago.
alternativesplicingtranscriptomicsvisualization
11.1 match 17 stars 6.74 score 18 scriptsbioc
profileplyr:Visualization and annotation of read signal over genomic ranges with profileplyr
Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.
Maintained by Tom Carroll. Last updated 5 months ago.
chipseqdataimportsequencingchiponchipcoverage
18.6 match 4.03 score 54 scriptsbioc
crisprShiny:Exploring curated CRISPR gRNAs via Shiny
Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.
Maintained by Jean-Philippe Fortin. Last updated 5 months ago.
crisprfunctionalgenomicsgenetargetguicrispr-analysiscrispr-designshiny
16.7 match 2 stars 4.48 score 8 scriptsjbkunst
highcharter:A Wrapper for the 'Highcharts' Library
A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.
Maintained by Joshua Kunst. Last updated 1 years ago.
highchartshtmlwidgetsshinyshiny-rvisualizationwrapper
5.4 match 725 stars 13.93 score 4.9k scripts 18 dependentsbioc
isomiRs:Analyze isomiRs and miRNAs from small RNA-seq
Characterization of miRNAs and isomiRs, clustering and differential expression.
Maintained by Lorena Pantano. Last updated 5 months ago.
mirnarnaseqdifferentialexpressionclusteringimmunooncologyanalyze-isomirsbioconductorisomirs
10.6 match 8 stars 7.09 score 43 scriptsbioc
myvariant:Accesses MyVariant.info variant query and annotation services
MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services
Maintained by Adam Mark, Chunlei Wu. Last updated 5 months ago.
variantannotationannotationgenomicvariation
15.1 match 4.92 score 28 scriptseltebioinformatics
mulea:Enrichment Analysis Using Multiple Ontologies and False Discovery Rate
Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.
Maintained by Tamas Stirling. Last updated 3 months ago.
annotationdifferentialexpressiongeneexpressiongenesetenrichmentgographandnetworkmultiplecomparisonpathwaysreactomesoftwaretranscriptionvisualizationenrichmentenrichment-analysisfunctional-enrichment-analysisgene-set-enrichmentontologiestranscriptomicscpp
10.0 match 28 stars 7.36 score 34 scriptsdigi-vub
recogito:Interactive Annotation of Text and Images
Annotate text with entities and the relations between them. Annotate areas of interest in images with your labels. Providing 'htmlwidgets' bindings to the 'recogito' <https://github.com/recogito/recogito-js> and 'annotorious' <https://github.com/recogito/annotorious> libraries.
Maintained by Jan Wijffels. Last updated 3 years ago.
17.3 match 21 stars 4.25 score 17 scriptsbioc
GenomicPlot:Plot profiles of next generation sequencing data in genomic features
Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. 'GenomicPlot' facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.
Maintained by Shuye Pu. Last updated 2 months ago.
alternativesplicingchipseqcoveragegeneexpressionrnaseqsequencingsoftwaretranscriptionvisualizationannotation
13.1 match 3 stars 5.62 score 4 scriptsbioc
NormalyzerDE:Evaluation of normalization methods and calculation of differential expression analysis statistics
NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.
Maintained by Jakob Willforss. Last updated 5 months ago.
normalizationmultiplecomparisonvisualizationbayesianproteomicsmetabolomicsdifferentialexpressionbioconductorbioinformaticslimma
10.0 match 22 stars 7.30 score 38 scripts 1 dependents