frattalab

bedops_parse_star_junctions

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

helpful_scripts

Helpful scripts for performing routine analyses

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

paqr_annotations

Snakemake workflow to generate annotation files for PAQR

pipeline_iclip

QAPA_snakemake

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

rna_seq_snakemake

Snakemake Pipeline For RNA-Seq in UCL Cluster

splicing

Snakemake pipeline for running MAJIQ

unc13a_cryptic_splicing

Figures for UNC13A paper

frattalab/splicing

Snakemake pipeline for running MAJIQ

frattalab/rna_seq_snakemake

Snakemake Pipeline For RNA-Seq in UCL Cluster

frattalab/unc13a_cryptic_splicing

Figures for UNC13A paper

frattalab/helpful_scripts

Helpful scripts for performing routine analyses

frattalab/pipeline_iclip

frattalab/paqr_annotations

Snakemake workflow to generate annotation files for PAQR

frattalab/bedops_parse_star_junctions

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

frattalab/hisat3_snakemake

quick snakemake pipeline for running hisat3n

frattalab/PAPA

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

frattalab/QAPA_snakemake

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

frattalab/SpliceNouveau

frattalab/downloading_from_sra

Simple code for downloading from SRA in a parallel manner

frattalab/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

frattalab/rna_seq_single_steps

Snakemake pipelines for common bioinformatics tasks

frattalab/tdp43-apa

Code for TDP-43 APA manuscript

frattalab/tectools_pipeline

snakemake pipeline to run tectools

frattalab/bookclub-islr

Introduction to Statistical Learning Using R Book Club

frattalab/differential-expression-

frattalab/GeneStructureTools

frattalab/leafcutter-pipeline

Differential splicing and visualisation pipeline for the Raj lab

frattalab/MicroExonator

Snakemake pipeline for microexon discovery and quantification