PAIRADISE

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.)

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 RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.

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.

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.

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.

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.