Showing 107 of total 107 results (show query)
bioc
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
67.4 match 36 stars 6.95 score 31 scriptsbioc
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
64.9 match 5.91 score 45 scripts 3 dependents
agi-lab
SPLICE:Synthetic Paid Loss and Incurred Cost Experience (SPLICE) Simulator
An extension to the individual claim simulator called 'SynthETIC' (on CRAN), to simulate the evolution of case estimates of incurred losses through the lifetime of an insurance claim. The transactional simulation output now comprises key dates, and both claim payments and revisions of estimated incurred losses. An initial set of test parameters, designed to mirror the experience of a real insurance portfolio, were set up and applied by default to generate a realistic test data set of incurred histories (see vignette). However, the distributional assumptions used to generate this data set can be easily modified by users to match their experiences. Reference: Avanzi B, Taylor G, Wang M (2021) "SPLICE: A Synthetic Paid Loss and Incurred Cost Experience Simulator" <arXiv:2109.04058>.
Maintained by Melantha Wang. Last updated 1 years ago.
61.1 match 6 stars 5.58 score 14 scriptsbioc
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
46.0 match 17 stars 6.74 score 18 scripts
cran
MARVEL:Revealing Splicing Dynamics at Single-Cell Resolution
Alternative splicing represents an additional and underappreciated layer of complexity underlying gene expression profiles. Nevertheless, there remains hitherto a paucity of software to investigate splicing dynamics at single-cell resolution. 'MARVEL' enables splicing analysis of single-cell RNA-sequencing data generated from plate- and droplet-based library preparation methods.
Maintained by Sean Wen. Last updated 2 years ago.
100.5 match 2.71 score 51 scriptsbioc
FRASER:Find RAre Splicing Events in RNA-Seq Data
Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.
Maintained by Christian Mertes. Last updated 5 months ago.
rnaseqalternativesplicingsequencingsoftwaregeneticscoverageaberrant-splicingdiagnosticsoutlier-detectionrare-diseaserna-seqsplicingopenblascpp
29.6 match 41 stars 8.50 score 155 scripts
jacekbialek
PriceIndices:Calculating Bilateral and Multilateral Price Indexes
Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020) <doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Maintained by Jacek Białek. Last updated 2 months ago.
35.8 match 11 stars 6.06 score 16 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
18.2 match 108 stars 9.26 score 125 scriptsbioc
EventPointer:An effective identification of alternative splicing events using junction arrays and RNA-Seq data
EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.
Maintained by Juan A. Ferrer-Bonsoms. Last updated 5 months ago.
alternativesplicingdifferentialsplicingmrnamicroarrayrnaseqtranscriptionsequencingtimecourseimmunooncology
27.5 match 4 stars 6.00 score 6 scripts
r-lib
rlang:Functions for Base Types and Core R and 'Tidyverse' Features
A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Maintained by Lionel Henry. Last updated 19 days ago.
7.3 match 517 stars 20.53 score 9.8k scripts 15k dependents
treynkens
ReIns:Functions from "Reinsurance: Actuarial and Statistical Aspects"
Functions from the book "Reinsurance: Actuarial and Statistical Aspects" (2017) by Hansjoerg Albrecher, Jan Beirlant and Jef Teugels <https://www.wiley.com/en-us/Reinsurance%3A+Actuarial+and+Statistical+Aspects-p-9780470772683>.
Maintained by Tom Reynkens. Last updated 4 months ago.
extremesreinsurancerisk-analysiscpp
21.1 match 22 stars 6.31 score 186 scriptsbioc
VaSP:Quantification and Visualization of Variations of Splicing in Population
Discovery of genome-wide variable alternative splicing events from short-read RNA-seq data and visualizations of gene splicing information for publication-quality multi-panel figures in a population. (Warning: The visualizing function is removed due to the dependent package Sushi deprecated. If you want to use it, please change back to an older version.)
Maintained by Huihui Yu. Last updated 5 months ago.
rnaseqalternativesplicingdifferentialsplicingstatisticalmethodvisualizationpreprocessingclusteringdifferentialexpressionkeggimmunooncology3s-scoresalternative-splicingballgownrna-seqsplicingsqtlstatistics
27.8 match 3 stars 4.78 score 3 scriptsbioc
limma:Linear Models for Microarray and Omics Data
Data analysis, linear models and differential expression for omics data.
Maintained by Gordon Smyth. Last updated 5 days ago.
exonarraygeneexpressiontranscriptionalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentdataimportbayesianclusteringregressiontimecoursemicroarraymicrornaarraymrnamicroarrayonechannelproprietaryplatformstwochannelsequencingrnaseqbatcheffectmultiplecomparisonnormalizationpreprocessingqualitycontrolbiomedicalinformaticscellbiologycheminformaticsepigeneticsfunctionalgenomicsgeneticsimmunooncologymetabolomicsproteomicssystemsbiologytranscriptomics
7.6 match 13.81 score 16k scripts 585 dependentsbioc
SplicingFactory:Splicing Diversity Analysis for Transcriptome Data
The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.
Maintained by Endre Sebestyen. Last updated 5 months ago.
transcriptomicsrnaseqdifferentialsplicingalternativesplicingtranscriptomevariantgini-indexrna-seqshannon-entropysimpson-indexsplicing
20.1 match 4 stars 5.20 score 1 scripts
tuomaseerola
movementsync:Analysis and Visualisation of Musical Audio and Video Movement Synchrony Data
Analysis and visualisation of synchrony, interaction, and joint movements from audio and video movement data of a group of music performers. The demo is data described in Clayton, Leante, and Tarsitani (2021) <doi:10.17605/OSF.IO/KS325>, while example analyses can be found in Clayton, Jakubowski, and Eerola (2019) <doi:10.1177/1029864919844809>. Additionally, wavelet analysis techniques have been applied to examine movement-related musical interactions, as shown in Eerola et al. (2018) <doi:10.1098/rsos.171520>.
Maintained by Tuomas Eerola. Last updated 1 years ago.
35.5 match 1 stars 2.85 score 14 scriptsbioc
edgeR:Empirical Analysis of Digital Gene Expression Data in R
Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage.
Maintained by Yunshun Chen. Last updated 5 days ago.
alternativesplicingbatcheffectbayesianbiomedicalinformaticscellbiologychipseqclusteringcoveragedifferentialexpressiondifferentialmethylationdifferentialsplicingdnamethylationepigeneticsfunctionalgenomicsgeneexpressiongenesetenrichmentgeneticsimmunooncologymultiplecomparisonnormalizationpathwaysproteomicsqualitycontrolregressionrnaseqsagesequencingsinglecellsystemsbiologytimecoursetranscriptiontranscriptomicsopenblas
7.3 match 13.40 score 17k scripts 255 dependentsbioc
SplicingGraphs:Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.
Maintained by H. Pagès. Last updated 5 months ago.
geneticsannotationdatarepresentationvisualizationsequencingrnaseqgeneexpressionalternativesplicingtranscriptionimmunooncologybioconductor-package
17.4 match 2 stars 5.26 score 8 scriptsbioc
SpliceWiz:interactive analysis and visualization of alternative splicing in R
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.
Maintained by Alex Chit Hei Wong. Last updated 3 days ago.
softwaretranscriptomicsrnaseqalternativesplicingcoveragedifferentialsplicingdifferentialexpressionguisequencingcppopenmp
14.1 match 16 stars 6.41 score 8 scriptsbioc
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
14.3 match 10 stars 5.78 score 5 scriptsbioc
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
18.3 match 4.32 score 21 scripts
tidyverse
purrr:Functional Programming Tools
A complete and consistent functional programming toolkit for R.
Maintained by Hadley Wickham. Last updated 1 months ago.
3.3 match 1.3k stars 22.12 score 59k scripts 6.9k dependentsbioc
saseR:Scalable Aberrant Splicing and Expression Retrieval
saseR is a highly performant and fast framework for aberrant expression and splicing analyses. The main functions are: \itemize{ \item \code{\link{BamtoAspliCounts}} - Process BAM files to ASpli counts \item \code{\link{convertASpli}} - Get gene, bin or junction counts from ASpli SummarizedExperiment \item \code{\link{calculateOffsets}} - Create an offsets assays for aberrant expression or splicing analysis \item \code{\link{saseRfindEncodingDim}} - Estimate the optimal number of latent factors to include when estimating the mean expression \item \code{\link{saseRfit}} - Parameter estimation of the negative binomial distribution and compute p-values for aberrant expression and splicing } For information upon how to use these functions, check out our vignette at \url{https://github.com/statOmics/saseR/blob/main/vignettes/Vignette.Rmd} and the saseR paper: Segers, A. et al. (2023). Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. bioRxiv. \url{https://doi.org/10.1101/2023.06.29.547014}.
Maintained by Alexandre Segers. Last updated 5 months ago.
differentialexpressiondifferentialsplicingregressiongeneexpressionalternativesplicingrnaseqsequencingsoftware
15.8 match 1 stars 4.40 score 1 scriptsbioc
SeqGSEA:Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.
Maintained by Xi Wang. Last updated 5 months ago.
sequencingrnaseqgenesetenrichmentgeneexpressiondifferentialexpressiondifferentialsplicingimmunooncology
15.6 match 4.34 score 11 scriptsbioc
casper:Characterization of Alternative Splicing based on Paired-End Reads
Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Maintained by David Rossell. Last updated 4 months ago.
immunooncologygeneexpressiondifferentialexpressiontranscriptionrnaseqsequencingcpp
12.1 match 5.02 score 66 scriptsbioc
BANDITS:BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.
Maintained by Simone Tiberi. Last updated 5 months ago.
differentialsplicingalternativesplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationopenblascpp
10.3 match 17 stars 5.75 score 11 scripts 1 dependentsbioc
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
10.4 match 5 stars 5.30 score 4 scriptsbioc
IMAS:Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative splicing.
Maintained by Seonggyun Han. Last updated 5 months ago.
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription
11.3 match 4.85 score 1 scriptsbioc
ASpli:Analysis of Alternative Splicing Using RNA-Seq
Integrative pipeline for the analysis of alternative splicing using RNAseq.
Maintained by Ariel Chernomoretz. Last updated 5 months ago.
immunooncologygeneexpressiontranscriptionalternativesplicingcoveragedifferentialexpressiondifferentialsplicingtimecoursernaseqgenomeannotationsequencingalignment
9.5 match 5.33 score 45 scripts 1 dependentsbioc
IVAS:Identification of genetic Variants affecting Alternative Splicing
Identification of genetic variants affecting alternative splicing.
Maintained by Seonggyun Han. Last updated 5 months ago.
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription
9.9 match 4.78 score 1 scripts 1 dependentsbioc
GenomicAlignments:Representation and manipulation of short genomic alignments
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
Maintained by Hervé Pagès. Last updated 5 months ago.
infrastructuredataimportgeneticssequencingrnaseqsnpcoveragealignmentimmunooncologybioconductor-packagecore-package
3.4 match 10 stars 13.61 score 3.1k scripts 529 dependentsbioc
Ularcirc:Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.
Maintained by David Humphreys. Last updated 5 months ago.
datarepresentationvisualizationgeneticssequencingannotationcoveragealternativesplicingdifferentialsplicing
10.1 match 4.30 score 4 scriptsbioc
OutSplice:Comparison of Splicing Events between Tumor and Normal Samples
An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.
Maintained by Theresa Guo. Last updated 1 months ago.
alternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressionrnaseqsoftwarevariantannotation
9.1 match 1 stars 4.30 score 4 scripts
gfellerlab
SuperCell:Simplification of scRNA-seq data by merging together similar cells
Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells.
Maintained by The package maintainer. Last updated 8 months ago.
softwarecoarse-grainingscrna-seq-analysisscrna-seq-data
4.8 match 72 stars 8.08 score 93 scriptsbioc
FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.
Maintained by Changqing Wang. Last updated 5 days ago.
rnaseqsinglecelltranscriptomicsdataimportdifferentialsplicingalternativesplicinggeneexpressionlongreadzlibcurlbzip2xz-utilscpp
4.5 match 31 stars 7.95 score 12 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
8.6 match 1 stars 4.00 score 2 scriptsbioc
snapcount:R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).
Maintained by Rone Charles. Last updated 5 months ago.
coveragegeneexpressionrnaseqsequencingsoftwaredataimport
6.1 match 3 stars 5.19 score 13 scripts
kurthornik
mlbench:Machine Learning Benchmark Problems
A collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository.
Maintained by Kurt Hornik. Last updated 3 months ago.
3.5 match 2 stars 8.93 score 5.0k scripts 55 dependents
pierreroudier
spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data
Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.
Maintained by Pierre Roudier. Last updated 2 years ago.
5.0 match 11 stars 6.17 score 45 scripts 1 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
7.3 match 4.00 score 2 scriptsbioc
ggbio:Visualization tools for genomic data
The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
Maintained by Michael Lawrence. Last updated 5 months ago.
2.3 match 111 stars 12.26 score 734 scripts 17 dependents
tidymodels
tune:Tidy Tuning Tools
The ability to tune models is important. 'tune' contains functions and classes to be used in conjunction with other 'tidymodels' packages for finding reasonable values of hyper-parameters in models, pre-processing methods, and post-processing steps.
Maintained by Max Kuhn. Last updated 12 days ago.
1.9 match 293 stars 14.27 score 756 scripts 39 dependentsbioc
TIN:Transcriptome instability analysis
The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.
Maintained by Bjarne Johannessen. Last updated 5 months ago.
exonarraymicroarraygeneexpressionalternativesplicinggeneticsdifferentialsplicing
6.2 match 4.30 score 1 scriptsbioc
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
5.2 match 4.88 score 17 scriptsbioc
powerTCR:Model-Based Comparative Analysis of the TCR Repertoire
This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.
Maintained by Hillary Koch. Last updated 5 months ago.
softwareclusteringbiomedicalinformatics
6.3 match 4.00 score 4 scriptsbioc
QuasR:Quantify and Annotate Short Reads in R
This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.
Maintained by Michael Stadler. Last updated 23 days ago.
geneticspreprocessingsequencingchipseqrnaseqmethylseqcoveragealignmentqualitycontrolimmunooncologycurlbzip2xz-utilszlibcpp
2.9 match 6 stars 8.70 score 79 scripts 1 dependents
r-forge
tframe:Time Frame Coding Kernel
A kernel of functions for programming time series methods in a way that is relatively independently of the representation of time. Also provides plotting, time windowing, and some other utility functions which are specifically intended for time series. See the Guide distributed as a vignette, or '?tframe.Intro' for more details. (User utilities are in package 'tfplot'.)
Maintained by Paul Gilbert. Last updated 1 years ago.
5.3 match 4.49 score 34 scripts 3 dependents
nvelden
geneviewer:Gene Cluster Visualizations
Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>; Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.
Maintained by Niels van der Velden. Last updated 29 days ago.
4.0 match 43 stars 5.86 score 13 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
3.6 match 8 stars 5.98 score 6 scriptsbioc
IntEREst:Intron-Exon Retention Estimator
This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).
Maintained by Ali Oghabian. Last updated 4 days ago.
softwarealternativesplicingcoveragedifferentialsplicingsequencingrnaseqalignmentnormalizationdifferentialexpressionimmunooncology
5.1 match 4.16 score 12 scriptsbioc
systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation
systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.
Maintained by Thomas Girke. Last updated 5 months ago.
geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
1.8 match 53 stars 11.56 score 344 scripts 3 dependentsbioc
eisaR:Exon-Intron Split Analysis (EISA) in R
Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.
Maintained by Michael Stadler. Last updated 2 months ago.
transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
2.8 match 16 stars 7.48 score 63 scriptsbioc
regsplice:L1-regularization based methods for detection of differential splicing
Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.
Maintained by Lukas M. Weber. Last updated 5 months ago.
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicingsequencingrnaseqmicroarrayexonarrayexperimentaldesignsoftware
3.4 match 3 stars 5.86 score 27 scripts
bergsmat
tablet:Tabulate Descriptive Statistics in Multiple Formats
Creates a table of descriptive statistics for factor and numeric columns in a data frame. Displays these by groups, if any. Highly customizable, with support for 'html' and 'pdf' provided by 'kableExtra'. Respects original column order, column labels, and factor level order. See ?tablet.data.frame and vignettes.
Maintained by Tim Bergsma. Last updated 4 months ago.
3.3 match 3 stars 5.57 score 26 scriptsbioc
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
3.0 match 5.92 score 209 scriptsbioc
maSigPro:Significant Gene Expression Profile Differences in Time Course Gene Expression Data
maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.
Maintained by Maria Jose Nueda. Last updated 5 months ago.
microarrayrna-seqdifferential expressiontimecourse
3.4 match 5.18 score 76 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
1.7 match 326 stars 10.49 score 240 scriptsbioc
VarCon:VarCon: an R package for retrieving neighboring nucleotides of an SNV
VarCon is an R package which converts the positional information from the annotation of an single nucleotide variation (SNV) (either referring to the coding sequence or the reference genomic sequence). It retrieves the genomic reference sequence around the position of the single nucleotide variation. To asses, whether the SNV could potentially influence binding of splicing regulatory proteins VarCon calcualtes the HEXplorer score as an estimation. Besides, VarCon additionally reports splice site strengths of splice sites within the retrieved genomic sequence and any changes due to the SNV.
Maintained by Johannes Ptok. Last updated 5 months ago.
functionalgenomicsalternativesplicing
4.3 match 4.00 score 5 scripts
meierluk
grplasso:Fitting User-Specified Models with Group Lasso Penalty
Fits user-specified (GLM-) models with group lasso penalty.
Maintained by Lukas Meier. Last updated 5 years ago.
3.6 match 4 stars 4.78 score 128 scripts 6 dependents
l-ramirez-lopez
prospectr:Miscellaneous Functions for Processing and Sample Selection of Spectroscopic Data
Functions to preprocess spectroscopic data and conduct (representative) sample selection/calibration sampling.
Maintained by Leonardo Ramirez-Lopez. Last updated 10 days ago.
chemometricsderivativesinfrarednear-infrarednirpedometricspreprocessingresamplesamplingsignalsoil-spectroscopyspectroscopyopenblascppopenmp
1.7 match 42 stars 10.00 score 326 scripts 4 dependents
meireles
spectrolab:Class and Methods for Spectral Data
Input/Output, processing and visualization of spectra taken with different spectrometers, including SVC (Spectra Vista), ASD and PSR (Spectral Evolution). Implements an S3 class spectra that other packages can build on. Provides methods to access, plot, manipulate, splice sensor overlap, vector normalize and smooth spectra.
Maintained by Jose Eduardo Meireles. Last updated 2 months ago.
2.3 match 16 stars 7.39 score 256 scriptsbioc
bambu:Context-Aware Transcript Quantification from Long Read RNA-Seq data
bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.
Maintained by Ying Chen. Last updated 1 months ago.
alignmentcoveragedifferentialexpressionfeatureextractiongeneexpressiongenomeannotationgenomeassemblyimmunooncologylongreadmultiplecomparisonnormalizationrnaseqregressionsequencingsoftwaretranscriptiontranscriptomicsbambubioconductorlong-readsnanoporenanopore-sequencingrna-seqrna-seq-analysistranscript-quantificationtranscript-reconstructioncpp
1.9 match 197 stars 9.03 score 91 scripts 1 dependentsbioc
SPLINTER:Splice Interpreter of Transcripts
Provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.
Maintained by Diana Low. Last updated 5 months ago.
immunooncologygeneexpressionrnaseqvisualizationalternativesplicing
3.9 match 4.30 score 1 scripts
lionel-
fontquiver:Set of Installed Fonts
Provides a set of fonts with permissive licences. This is useful when you want to avoid system fonts to make sure your outputs are reproducible.
Maintained by Lionel Henry. Last updated 6 years ago.
1.9 match 17 stars 8.73 score 14 scripts 147 dependents
yeyuan98
gsAnalysis:Miscellaneous tools for genomic sequence analysis
A miscellaneous toolbox for various genomic sequence analysis tasks. Refer to package vignettes for different topics covered in this package. Part of the y3628 analysis suite.
Maintained by Ye Yuan. Last updated 2 months ago.
6.0 match 2.70 score 1 scriptsbioc
biovizBase:Basic graphic utilities for visualization of genomic data.
The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
Maintained by Michael Lawrence. Last updated 5 months ago.
infrastructurevisualizationpreprocessing
2.0 match 8.04 score 273 scripts 75 dependentsbioc
TransView:Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.
Maintained by Julius Muller. Last updated 2 months ago.
immunooncologydnamethylationgeneexpressiontranscriptionmicroarraysequencingchipseqrnaseqmethylseqdataimportvisualizationclusteringmultiplecomparisoncurlbzip2xz-utilszlib
6.0 match 2.60 score
cdueben
cppcontainers:'C++' Standard Template Library Containers
Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps, unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.
Maintained by Christian Düben. Last updated 2 months ago.
3.3 match 4.70 score 1 scriptsbioc
transmogR:Modify a set of reference sequences using a set of variants
transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.
Maintained by Stevie Pederson. Last updated 26 days ago.
alignmentgenomicvariationsequencingtranscriptomevariantzlib
3.3 match 4.70 score 2 scriptsbioc
ngsReports:Load FastqQC reports and other NGS related files
This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.
Maintained by Stevie Pederson. Last updated 5 months ago.
1.9 match 22 stars 7.89 score 99 scriptsbioc
Rhisat2:R Wrapper for HISAT2 Aligner
An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Maintained by Charlotte Soneson. Last updated 3 months ago.
alignmentsequencingsplicedalignmentcpp
2.4 match 4 stars 6.08 score 7 scripts 1 dependentstidymodels
tidyclust:A Common API to Clustering
A common interface to specifying clustering models, in the same style as 'parsnip'. Creates unified interface across different functions and computational engines.
Maintained by Emil Hvitfeldt. Last updated 2 months ago.
1.9 match 111 stars 7.45 score 139 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
1.2 match 220 stars 11.80 score 578 scripts 3 dependentsbioc
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
1.3 match 33 stars 10.63 score 115 scripts 2 dependents
marberts
gpindex:Generalized Price and Quantity Indexes
Tools to build and work with bilateral generalized-mean price indexes (and by extension quantity indexes), and indexes composed of generalized-mean indexes (e.g., superlative quadratic-mean indexes, GEKS). Covers the core mathematical machinery for making bilateral price indexes, computing price relatives, detecting outliers, and decomposing indexes, with wrappers for all common (and many uncommon) index-number formulas. Implements and extends many of the methods in Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007, <doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020, <doi:10.5089/9781484354841.069>).
Maintained by Steve Martin. Last updated 2 days ago.
economicsinflationofficial-statisticsstatistics
2.0 match 7 stars 6.63 score 29 scripts 1 dependentsbioc
Rbowtie:R bowtie wrapper
This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.
Maintained by Michael Stadler. Last updated 2 months ago.
1.8 match 1 stars 6.80 score 22 scripts 8 dependents
rmgpanw
gtexr:Query the GTEx Portal API
A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. For more information on the API, see <https://gtexportal.org/api/v2/redoc>.
Maintained by Alasdair Warwick. Last updated 6 months ago.
api-wrapperbioinformaticseqtlgtexsqtl
1.8 match 5 stars 6.41 score 5 scriptsbioc
branchpointer:Prediction of intronic splicing branchpoints
Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.
Maintained by Beth Signal. Last updated 5 months ago.
softwaregenomeannotationgenomicvariationmotifannotation
3.1 match 3.62 score 21 scriptsbioc
GSReg:Gene Set Regulation (GS-Reg)
A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).
Maintained by Bahman Afsari. Last updated 5 months ago.
generegulationpathwaysgeneexpressiongeneticvariabilitygenesetenrichmentalternativesplicing
2.8 match 3.98 score 16 scriptsbioc
seqTools:Analysis of nucleotide, sequence and quality content on fastq files
Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.
Maintained by Wolfgang Kaisers. Last updated 5 months ago.
1.6 match 5.57 score 52 scripts 1 dependentsbioc
BiGGR:Constraint based modeling in R using metabolic reconstruction databases
This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.
Maintained by Anand K. Gavai. Last updated 5 months ago.
systems biologypathwaynetworkgraphandnetworkvisualizationmetabolomics
1.9 match 4.67 score 58 scripts
greymonroe
genemodel:Gene Model Plotting in R
Using simple input, this package creates plots of gene models. Users can create plots of alternatively spliced gene variants and the positions of mutations and other gene features.
Maintained by J Grey Monroe. Last updated 8 years ago.
2.0 match 4 stars 4.30 score 9 scriptsbioc
PECA:Probe-level Expression Change Averaging
Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.
Maintained by Tomi Suomi. Last updated 5 months ago.
softwareproteomicsmicroarraydifferentialexpressiongeneexpressionexonarraydifferentialsplicing
2.0 match 4.34 score 11 scripts
skranz
gtree:gtree basic functionality to model and solve games
gtree basic functionality to model and solve games
Maintained by Sebastian Kranz. Last updated 4 years ago.
economic-experimentseconomicsgambitgame-theorynash-equilibrium
2.3 match 18 stars 3.79 score 23 scripts 1 dependentsbioc
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
1.7 match 1 stars 5.02 score 2 scriptsbioc
DuplexDiscovereR:Analysis of the data from RNA duplex probing experiments
DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.
Maintained by Egor Semenchenko. Last updated 2 months ago.
sequencingtranscriptomicsstructuralpredictionclusteringsplicedalignment
1.8 match 1 stars 4.60 score 5 scriptsbioc
annmap:Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071
Maintained by Chris Wirth. Last updated 5 months ago.
annotationmicroarrayonechannelreportwritingtranscriptionvisualization
2.3 match 3.00 score 2 scripts
bioc
PAIRADISE:PAIRADISE: Paired analysis of differential isoform expression
This package implements the PAIRADISE procedure for detecting differential isoform expression between matched replicates in paired RNA-Seq data.
Maintained by Qiang Hu. Last updated 5 months ago.
rnaseqdifferentialexpressionalternativesplicingstatisticalmethodimmunooncology
1.6 match 3.30 score 7 scriptscran
comato:Analysis of Concept Maps and Concept Landscapes
Provides methods for the import/export and automated analysis of concept maps and concept landscapes (sets of concept maps).
Maintained by Andreas Muehling. Last updated 7 years ago.
3.3 match 1.56 score 36 scriptsbioc
DifferentialRegulation:Differentially regulated genes from scRNA-seq data
DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) 'ambiguous' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).
Maintained by Simone Tiberi. Last updated 5 months ago.
differentialsplicingbayesiangeneticsrnaseqsequencingdifferentialexpressiongeneexpressionmultiplecomparisonsoftwaretranscriptionstatisticalmethodvisualizationsinglecellgenetargetopenblascpp
0.9 match 10 stars 5.30 score 4 scripts
prabinameher
EncDNA:Encoding of Nucleotide Sequences into Numeric Feature Vectors
We describe fifteen different splice site sequence encoding schemes that have been used in earlier studies for mapping of splice site sequences into numeric feature vectors. These encoding schemes will also be helpful for transforming other nucleotide sequences into numeric forms, provided they are of equal length. These encoding schemes will help the computational biologist working in the field of classification (binary or multiclass) or prediction involving nucleic acid sequences of equal length.
Maintained by Prabina Kumar Meher. Last updated 6 years ago.
4.1 match 1 stars 1.00 scorebioc
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
0.5 match 9 stars 7.35 score 165 scriptsprabinameher
corrDNA:Finding Associations in Position-Wise Aligned DNA Sequence Dataset
Can be useful for finding associations among different positions in a position-wise aligned sequence dataset. The approach adopted for finding associations among positions is based on the latent multivariate normal distribution.
Maintained by Prabina Kumar Meher. Last updated 7 years ago.
3.5 match 1.00 score 8 scriptsbioc
VariantFiltering:Filtering of coding and non-coding genetic variants
Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.
Maintained by Robert Castelo. Last updated 1 months ago.
geneticshomo_sapiensannotationsnpsequencinghighthroughputsequencing
0.5 match 4 stars 6.23 score 21 scripts
grahamjwhite
IndexNumR:Index Number Calculation
Computes bilateral and multilateral index numbers. It has support for many standard bilateral indexes as well as multilateral index number methods such as GEKS, GEKS-Tornqvist (or CCDI), Geary-Khamis and the weighted time product dummy (for details on these methods see Diewert and Fox (2020) <doi:10.1080/07350015.2020.1816176>). It also supports updating of multilateral indexes using several splicing methods.
Maintained by Graham White. Last updated 1 years ago.
0.5 match 15 stars 6.20 score 71 scripts 1 dependentsbioc
kissDE:Retrieves Condition-Specific Variants in RNA-Seq Data
Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of 'KisSplice' but can also be used with user's own data.
Maintained by Aurélie Siberchicot. Last updated 5 months ago.
alternativesplicingdifferentialsplicingexperimentaldesigngenomicvariationrnaseqtranscriptomics
0.5 match 3 stars 5.98 score 7 scriptsbioc
surfaltr:Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.
Maintained by Pooja Gangras. Last updated 5 months ago.
softwarevisualizationdatarepresentationsplicedalignmentalignmentmultiplesequencealignmentmultiplecomparison
0.8 match 4.00 score 2 scriptsbioc
ExCluster:ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.
Maintained by R. Matthew Tanner. Last updated 5 months ago.
immunooncologydifferentialsplicingrnaseqsoftware
0.9 match 3.30 score 1 scriptsbioc
puma:Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.
Maintained by Xuejun Liu. Last updated 5 months ago.
microarrayonechannelpreprocessingdifferentialexpressionclusteringexonarraygeneexpressionmrnamicroarraychiponchipalternativesplicingdifferentialsplicingbayesiantwochanneldataimporthta2.0
0.5 match 4.53 score 17 scripts
bioc
RgnTX:Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.
Maintained by Yue Wang. Last updated 5 months ago.
alternativesplicingsequencingrnaseqmethylseqtranscriptionsplicedalignment
0.5 match 4.00 score 6 scripts
bioc
GeneRegionScan:GeneRegionScan
A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.
Maintained by Lasse Folkersen. Last updated 5 months ago.
microarraydataimportsnponechannelvisualization
0.5 match 3.78 score 1 scriptsbioc
pairedGSEA:Paired DGE and DGS analysis for gene set enrichment analysis
pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.
Maintained by Søren Helweg Dam. Last updated 1 months ago.
differentialexpressionalternativesplicingdifferentialsplicinggeneexpressionimmunooncologygenesetenrichmentpathwaysrnaseqsoftwaretranscription
0.5 match 2 stars 3.48 scorecran
RHybridFinder:Identification of Hybrid Peptides in Immunopeptidomic Analyses
Tool for the analysis Mass Spectrometry (MS) data in the context of immunopeptidomic analysis for the identification of hybrid peptides and the predictions of binding affinity of all peptides using 'netMHCpan' <doi:10.1093/nar/gkaa379> while providing a summary of the netMHCpan output. 'RHybridFinder' (RHF) is destined for researchers who are looking to analyze their MS data for the purpose of identification of potential spliced peptides. This package, developed mainly in base R, is based on the workflow published by Faridi et al. in 2018 <doi:10.1126/sciimmunol.aar3947>.
Maintained by Frederic Saab. Last updated 4 years ago.
0.5 match 2.00 score