Lightweight and Fast; RNA-seq quantification at the event-level

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

BRIE: Bayesian Regression for Isoform Estimate

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Vials is a Caleydo Web application for visualizing alternative splicing based on mRNAseq data.

Discover differential transcript usage from polyA-captured single cell RNA-seq data

⚔️Find splicing-led, functional changes of the proteome.

NGS Tutorial

Pathway Enrichment-Guided Activity Study of Alternative Splicing (PEGASAS)

A tool to model the evolution and structural impact of alternative splicing

Docker to run rMATS for splicing quantification and analysis

Performing Cancer Diagnosis via an Isoform Level Expression Ranking-based LSTM Model

Alternative splicing event annotation for Human assembly (hg38)

An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.

A supervised methodology for analyzing dysregulation in splicing machinery: an application in cancer diagnosis.

Reproducibility of "Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues."

Use Thor's Axe to cut exons into their evolutionary building blocks ⚡

Computational biology pipeline that quantifies RNA splicing and performs sQTL mapping

Reading Genomic Files and provide data as API

Dynamic Isoform spliCing Estimator via sequencing data

Alternative splicing event annotation for Human assembly (hg19)

A snakemake workflow to perform Alternative Splicing analysis from RNA-Seq with SUPPA2.

The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction

Docker to run Whippet for splicing quantification and analysis

Docker to run VAST-TOOLS for splicing quantification and analysis

Docker to run MISO for splicing quantification and analysis

My personal snakemake pipeline for VAST-TOOLS execution