Showing 48 of total 48 results (show query)
schoonees
cds:Constrained Dual Scaling for Detecting Response Styles
This is an implementation of constrained dual scaling for detecting response styles in categorical data, including utility functions. The procedure involves adding additional columns to the data matrix representing the boundaries between the rating categories. The resulting matrix is then doubled and analyzed by dual scaling. One-dimensional solutions are sought which provide optimal scores for the rating categories. These optimal scores are constrained to follow monotone quadratic splines. Clusters are introduced within which the response styles can vary. The type of response style present in a cluster can be diagnosed from the optimal scores for said cluster, and this can be used to construct an imputed version of the data set which adjusts for response styles.
Maintained by Pieter Schoonees. Last updated 9 years ago.
71.3 match 2.65 score 37 scripts 1 dependents
bluegreen-labs
ecmwfr:Interface to 'ECMWF' and 'CDS' Data Web Services
Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Data Stores. Allows for easy downloads of weather forecasts and climate reanalysis data in R. Data stores covered include the Climate Data Store (CDS; <https://cds.climate.copernicus.eu>), Atmosphere Data Store (ADS; <https://ads.atmosphere.copernicus.eu>) and Early Warning Data Store (CEMS; <https://ewds.climate.copernicus.eu>).
Maintained by Koen Hufkens. Last updated 1 months ago.
cdsclimate-datacopernicusecmwf-apiecmwf-services
18.3 match 111 stars 10.08 score 156 scripts 3 dependents
ropensci
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
12.0 match 218 stars 11.35 score 129 scripts 3 dependents
uclahs-cds
BoutrosLab.plotting.general:Functions to Create Publication-Quality Plots
Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.
Maintained by Paul Boutros. Last updated 5 months ago.
15.0 match 12 stars 8.36 score 414 scripts 6 dependents
bioc
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. Pagès. Last updated 4 months ago.
geneticsinfrastructureannotationsequencinggenomeannotationbioconductor-packagecore-package
7.3 match 26 stars 15.34 score 5.3k scripts 339 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 10 days ago.
crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design
11.6 match 22 stars 8.28 score 80 scripts 3 dependentsuclahs-cds
CancerEvolutionVisualization:Publication Quality Phylogenetic Tree Plots
Generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user.
Maintained by Paul Boutros. Last updated 1 days ago.
15.0 match 2 stars 6.34 score 5 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
7.1 match 33 stars 10.63 score 115 scripts 2 dependents
yanrong-stacy-song
creditr:Credit Default Swaps
Price credit default swaps using 'C' code from the International Swaps and Derivatives Association CDS Standard Model. See <https://www.cdsmodel.com/cdsmodel/documentation.html> for more information about the model and <https://www.cdsmodel.com/cdsmodel/cds-disclaimer.html> for license details for the 'C' code.
Maintained by Yanrong Song. Last updated 19 days ago.
14.4 match 4.98 score 32 scripts
mt1022
cubar:Codon Usage Bias Analysis
A suite of functions for rapid and flexible analysis of codon usage bias. It provides in-depth analysis at the codon level, including relative synonymous codon usage (RSCU), tRNA weight calculations, machine learning predictions for optimal or preferred codons, and visualization of codon-anticodon pairing. Additionally, it can calculate various gene- specific codon indices such as codon adaptation index (CAI), effective number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation index (tAI), mean codon stabilization coefficients (CSCg), and GC contents (GC/GC3s/GC4d). It also supports both standard and non-standard genetic code tables found in NCBI, as well as custom genetic code tables.
Maintained by Hong Zhang. Last updated 3 months ago.
bioinformaticscodon-usagemachine-learningsequence-analysis
11.8 match 6 stars 5.82 score 8 scripts
junjunlab
ClusterGVis:One-Step to Cluster and Visualize Gene Expression Data
Streamlining the clustering and visualization of time-series gene expression data from RNA-Seq experiments, this tool supports fuzzy c-means and k-means clustering algorithms. It is compatible with outputs from widely-used packages such as 'Seurat', 'Monocle', and 'WGCNA', enabling seamless downstream visualization and analysis. See Lokesh Kumar and Matthias E Futschik (2007) <doi:10.6026/97320630002005> for more details.
Maintained by Jun Zhang. Last updated 6 days ago.
sequencingclusterprofilersummarizedexperimentmfuzzcomplexheatmapgene-clusteringgene-expressionvisualization
9.0 match 281 stars 6.80 score 30 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
13.1 match 2 stars 4.48 score 8 scriptsbioc
factR:Functional Annotation of Custom Transcriptomes
factR contain tools to process and interact with custom-assembled transcriptomes (GTF). At its core, factR constructs CDS information on custom transcripts and subsequently predicts its functional output. In addition, factR has tools capable of plotting transcripts, correcting chromosome and gene information and shortlisting new transcripts.
Maintained by Fursham Hamid. Last updated 5 months ago.
alternativesplicingfunctionalpredictiongenepredictioncustom-transcriptomesfunctional-annotationgtfrna-seq-analysis
14.3 match 1 stars 4.00 score 5 scriptsbioc
cicero:Predict cis-co-accessibility from single-cell chromatin accessibility data
Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.
Maintained by Hannah Pliner. Last updated 5 months ago.
sequencingclusteringcellbasedassaysimmunooncologygeneregulationgenetargetepigeneticsatacseqsinglecell
8.6 match 5.80 score 312 scriptsbioc
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
3.4 match 35 stars 14.08 score 892 scripts 108 dependentsbioc
sitePath:Phylogeny-based sequence clustering with site polymorphism
Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.
Maintained by Chengyang Ji. Last updated 5 months ago.
alignmentmultiplesequencealignmentphylogeneticssnpsoftwaremutationcpp
6.8 match 8 stars 5.20 score 9 scripts
distancedevelopment
mrds:Mark-Recapture Distance Sampling
Animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator.
Maintained by Laura Marshall. Last updated 2 months ago.
4.3 match 4 stars 8.05 score 78 scripts 7 dependentsbioc
ribosomeProfilingQC:Ribosome Profiling Quality Control
Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.
Maintained by Jianhong Ou. Last updated 1 months ago.
riboseqsequencinggeneregulationqualitycontrolvisualizationcoverage
6.8 match 4.88 score 17 scripts
pecanproject
PEcAn.data.land:PEcAn Functions Used for Ecological Forecasts and Reanalysis
The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.
Maintained by Mike Dietze. Last updated 1 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
3.4 match 216 stars 9.32 score 19 scripts 10 dependentsbioc
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 1 months ago.
alternativesplicingchipseqcoveragegeneexpressionrnaseqsequencingsoftwaretranscriptionvisualizationannotation
5.1 match 3 stars 5.62 score 4 scripts
cran
CreditRisk:Evaluation of Credit Risk with Structural and Reduced Form Models
Evaluation of default probability of sovereign and corporate entities based on structural or intensity based models and calibration on market Credit Default Swap quotes. References: Damiano Brigo, Massimo Morini, Andrea Pallavicini (2013) <doi:10.1002/9781118818589>. Print ISBN: 9780470748466, Online ISBN: 9781118818589. © 2013 John Wiley & Sons Ltd.
Maintained by Alessandro Cimarelli. Last updated 11 months ago.
16.5 match 3 stars 1.59 score 13 scriptsbioc
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.
3.3 match 7.45 score 34 scripts 35 dependentsbioc
doubletrouble:Identification and classification of duplicated genes
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.
Maintained by Fabrício Almeida-Silva. Last updated 3 days ago.
softwarewholegenomecomparativegenomicsfunctionalgenomicsphylogeneticsnetworkclassificationbioinformaticscomparative-genomicsgene-duplicationmolecular-evolutionwhole-genome-duplication
3.6 match 23 stars 6.44 score 17 scriptsbioc
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
3.3 match 3 stars 6.77 score 63 scripts 1 dependentsbioc
cummeRbund:Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
Maintained by Loyal A. Goff. Last updated 5 months ago.
highthroughputsequencinghighthroughputsequencingdatarnaseqrnaseqdatageneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationbioinformaticsclusteringmultiplecomparisonsqualitycontrol
3.3 match 5.92 score 209 scriptsbioc
APAlyzer:A toolkit for APA analysis using RNA-seq data
Perform 3'UTR APA, Intronic APA and gene expression analysis using RNA-seq data.
Maintained by Ruijia Wang. Last updated 5 months ago.
sequencingrnaseqdifferentialexpressiongeneexpressiongeneregulationannotationdataimportsoftwareative-polyadenylationbioinformatics-toolrna-seq
3.3 match 8 stars 5.81 score 9 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 1 months ago.
annotationgenomeannotationdataimportpreprocessingrnaseqsinglecelltranscriptomicstranscriptiongeneexpressionfunctionalgenomicsreproducibleresearchreportwritingimmunooncology
1.8 match 67 stars 10.58 score 466 scripts 1 dependents
jdieramon
refseqR:Common Computational Operations Working with RefSeq Entries (GenBank)
Fetches NCBI data (RefSeq <https://www.ncbi.nlm.nih.gov/refseq/> database) and provides an environment to extract information at the level of gene, mRNA or protein accessions.
Maintained by Jose V. Die. Last updated 3 months ago.
3.5 match 4 stars 5.34 score 5 scripts
blaserlab
blaseRdata:Supporting Data for the blaseRtools Package
What the package does (one paragraph).
Maintained by Brad Blaser. Last updated 12 months ago.
10.6 match 1.70 score 6 scriptsbioc
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
1.8 match 108 stars 9.26 score 125 scripts
dobrowski
MCOE:Creates New Folders and Loads Standard Practices for Monterey County Office of Education
Basic Setup for Projects in R for Monterey County Office of Education. It contains functions often used in the analysis of education data in the county office including seeing if an item is not in a list, rounding in the manner the general public expects, including logos for districts, switching between district names and their county-district-school codes, accessing the local 'SQL' table and making thematically consistent graphs.
Maintained by David Dobrowski. Last updated 1 years ago.
5.3 match 1 stars 3.11 score 26 scriptsbioc
ModCon:Modifying splice site usage by changing the mRNP code, while maintaining the genetic code
Collection of functions to calculate a nucleotide sequence surrounding for splice donors sites to either activate or repress donor usage. The proposed alternative nucleotide sequence encodes the same amino acid and could be applied e.g. in reporter systems to silence or activate cryptic splice donor sites.
Maintained by Johannes Ptok. Last updated 5 months ago.
functionalgenomicsalternativesplicing
4.0 match 1 stars 4.00 score 2 scriptsbioc
monocle:Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
Maintained by Cole Trapnell. Last updated 5 months ago.
immunooncologysequencingrnaseqgeneexpressiondifferentialexpressioninfrastructuredataimportdatarepresentationvisualizationclusteringmultiplecomparisonqualitycontrolcpp
1.8 match 8.89 score 1.6k scripts 2 dependentsbioc
CINdex:Chromosome Instability Index
The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.
Maintained by Yuriy Gusev. Last updated 5 months ago.
softwarecopynumbervariationgenomicvariationacghmicroarraygeneticssequencing
3.8 match 4.08 score 2 scriptsbioc
chimeraviz:Visualization tools for gene fusions
chimeraviz manages data from fusion gene finders and provides useful visualization tools.
Maintained by Stian Lågstad. Last updated 5 months ago.
1.8 match 37 stars 6.71 score 14 scripts
agrdatasci
ag5Tools:Toolbox for Downloading and Extracting Copernicus AgERA5 Data
Tools for downloading and extracting data from the Copernicus "Agrometeorological indicators from 1979 to present derived from reanalysis" <https://cds.climate.copernicus.eu/cdsapp#!/dataset/sis-agrometeorological-indicators?tab=overview> (AgERA5).
Maintained by David Brown. Last updated 4 months ago.
agriculture-researchagrometeorologicalclimate-data
1.8 match 8 stars 5.32 score 13 scriptsbioc
ProteoDisco:Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.
Maintained by Job van Riet. Last updated 5 months ago.
softwareproteomicsrnaseqsnpsequencingvariantannotationdataimport
1.8 match 5 stars 5.30 score 4 scriptsbioc
RiboProfiling:Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.
Maintained by A. Popa. Last updated 5 months ago.
riboseqsequencingcoveragealignmentqualitycontrolsoftwareprincipalcomponent
2.1 match 4.30 score 10 scriptsbioc
ribor:An R Interface for Ribo Files
The ribor package provides an R Interface for .ribo files. It provides functionality to read the .ribo file, which is of HDF5 format, and performs common analyses on its contents.
Maintained by Michael Geng. Last updated 5 months ago.
1.8 match 4.51 score 32 scripts
bioc
GeneStructureTools:Tools for spliced gene structure manipulation and analysis
GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.
Maintained by Beth Signal. Last updated 5 months ago.
immunooncologysoftwaredifferentialsplicingfunctionalpredictiontranscriptomicsalternativesplicingrnaseq
1.7 match 4.32 score 21 scriptsbioc
InPAS:Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.
Maintained by Jianhong Ou. Last updated 2 months ago.
alternative polyadenylationdifferential polyadenylation site usagerna-seqgene regulationtranscription
1.7 match 4.30 score 1 scripts
kwb-r
kwb.satellite:R Package for Working with Satellite Data from Various Providers (Copernicus, GoogleEarthEngine)
R Package with functions for working with satellite data of Copernicus Climate Data Store (https://cds.climate.copernicus.eu) or GoogleEarthEngine (https://earthengine.google.com/).
Maintained by Michael Rustler. Last updated 3 years ago.
copernicuscopernicus-climate-data-storegoogle-earth-engineproject-keyssatellite-data
1.8 match 1 stars 3.00 score 2 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. Pagès. Last updated 4 months ago.
infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package
0.5 match 3 stars 9.70 score 92 scripts 86 dependents
blenezet
credule:Credit Default Swap Functions
It provides functions to bootstrap Credit Curves from market quotes (Credit Default Swap - CDS - spreads) and price Credit Default Swaps - CDS.
Maintained by Bertrand Le Nezet. Last updated 10 years ago.
0.8 match 6 stars 4.52 score 11 scripts
mahito-sugiyama
graphkernels:Graph Kernels
A fast C++ implementation for computing various graph kernels including (1) simple kernels between vertex and/or edge label histograms, (2) graphlet kernels, (3) random walk kernels (popular baselines), and (4) the Weisfeiler-Lehman graph kernel (state-of-the-art).
Maintained by Mahito Sugiyama. Last updated 3 years ago.
1.6 match 1.68 score 48 scripts
lauren-hanna
Map2NCBI:Mapping Markers to the Nearest Genomic Feature
Allows the user to generate a list of features (gene, pseudo, RNA, CDS, and/or UTR) directly from NCBI database for any species with a current build available. Option to save downloaded and formatted files is available, and the user can prioritize the feature list based on type and assembly builds present in the current build used. The user can then use the list of features generated or provide a list to map a set of markers (designed for SNP markers with a single base pair position available) to the closest feature based on the map build. This function does require map positions of the markers to be provided and the positions should be based on the build being queried through NCBI.
Maintained by Lauren Hanna. Last updated 5 years ago.
0.5 match 1.30 score 6 scripts