frattalab

splicing

Snakemake pipeline for running MAJIQ

rna_seq_snakemake

Snakemake Pipeline For RNA-Seq in UCL Cluster

unc13a_cryptic_splicing

Figures for UNC13A paper

helpful_scripts

Helpful scripts for performing routine analyses

pipeline_iclip

paqr_annotations

Snakemake workflow to generate annotation files for PAQR

bedops_parse_star_junctions

Pipeline for taking STAR's SJ.out files and parsing the counts for a given bed of named spliced junctions

hisat3_snakemake

quick snakemake pipeline for running hisat3n

PAPA

PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data

QAPA_snakemake

Snakemake pipeline to run QAPA and perform differential polyA site usage analysis

downloading_from_sra

Simple code for downloading from SRA in a parallel manner

PAQR_KAPAC

scripts, pipelines and documentation to run PAQR and KAPAC; KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes; PAQR enables the quantification of poly(A) site usage from standard RNA-seq data

rna_seq_single_steps

Snakemake pipelines for common bioinformatics tasks

tdp43-apa

Code for TDP-43 APA manuscript

tectools_pipeline

snakemake pipeline to run tectools

bookclub-islr

Introduction to Statistical Learning Using R Book Club

differential-expression-

GeneStructureTools

leafcutter-pipeline

Differential splicing and visualisation pipeline for the Raj lab

MicroExonator

Snakemake pipeline for microexon discovery and quantification

SpliceNouveau