Bioconductor Packages

Analysis of Alternative Splicing Using RNA-Seq

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Inference of differential exon usage in RNA-Seq

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Find RAre Splicing Events in RNA-Seq Data

Gene Set Regulation (GS-Reg)

Tools for spliced gene structure manipulation and analysis

Plot profiles of next generation sequencing data in genomic features

Integrative analysis of Multi-omics data for Alternative Splicing

Identification of genetic Variants affecting Alternative Splicing

Intron-Exon Retention Estimator

IsoBayes: Single Isoform protein inference Method via Bayesian Analyses

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

Comparison of Splicing Events between Tumor and Normal Samples

PAIRADISE: Paired analysis of differential isoform expression

Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

Splice event prediction and quantification from RNA-seq data

Splice Interpreter of Transcripts

An R package to identify functional impacts due to alternative RNA processing events

interactive analysis and visualization of alternative splicing in R

Splicing Diversity Analysis for Transcriptome Data

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Transcriptome instability analysis

Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Quantification and Visualization of Variations of Splicing in Population

VarCon: an R package for retrieving neighboring nucleotides of an SNV

Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Empirical Analysis of Digital Gene Expression Data in R

Assess Differential Gene Expression Experiments with ERCC Controls

Functional Annotation of Custom Transcriptomes

Fishpond: downstream methods and tools for expression data

Retrieves Condition-Specific Variants in RNA-Seq Data

Linear Models for Microarray and Omics Data

Mapping Alternative Splicing Events to pRoteins

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Paired DGE and DGS analysis for gene set enrichment analysis

Identification of domain isotypes in pfam data

Estimate Promoter Activity from RNA-Seq data

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

L1-regularization based methods for detection of differential splicing

Rotation based gene set analysis

Scalable Aberrant Splicing and Expression Retrieval

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

splicelogic: differential transcripts to splice events

Make read coverage plots from BigWig files