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    24 repositories

    • rna_seq_snakemake

      Public
      Snakemake Pipeline For RNA-Seq in UCL Cluster
      Python
      •5•10•8•1•Updated Aug 5, 2026Aug 5, 2026

    • cryptic_biology

      Public
      Analysis code for the cryptic biology paper
      HTML
      •0•0•1•0•Updated May 12, 2026May 12, 2026

    • junction_explorer

      Public
      Shiny app for exploring junction
      R
      •1•1•0•0•Updated Nov 20, 2025Nov 20, 2025

    • trackplot_snakemake

      Public
      Snakemake pipeline for trackplot to make coverage track plots across a series of intervals
      Python
      •1•0•0•0•Updated May 22, 2025May 22, 2025

    • rna_seq_single_steps

      Public
      Snakemake pipelines for common bioinformatics tasks
      Python
      •
      MIT License
      •2•0•1•0•Updated Apr 14, 2025Apr 14, 2025

    • tdp43-apa

      Public
      Code for TDP-43 cryptic APA manuscript
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Apr 14, 2025Apr 14, 2025

    • PAPA

      Public
      PAPA (Pipeline-Alternative Polyadenylation) - Snakemake pipeline for analysis of APA from short-read RNA-seq data
      Python
      •
      GNU General Public License v3.0
      •0•2•16•1•Updated Apr 14, 2025Apr 14, 2025

    • QAPA_snakemake

      Public
      Snakemake pipeline to run QAPA and perform differential polyA site usage analysis
      Python
      •
      MIT License
      •1•1•5•0•Updated Jan 9, 2025Jan 9, 2025

    • SpliceNouveau

      Public
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Aug 13, 2024Aug 13, 2024

    • splicing

      Public
      Snakemake pipeline for running MAJIQ
      R
      •7•23•2•0•Updated Dec 20, 2023Dec 20, 2023

    • bedops_parse_star_junctions

      Public
      Pipeline for taking STAR's SJ.out files and parsing the counts for a given bed of named spliced junctions
      Python
      •2•3•0•0•Updated Sep 19, 2023Sep 19, 2023

    • hisat3_snakemake

      Public
      quick snakemake pipeline for running hisat3n
      Python
      •0•1•0•0•Updated Feb 21, 2023Feb 21, 2023

    • helpful_scripts

      Public
      Helpful scripts for performing routine analyses
      R
      •0•3•0•0•Updated Mar 18, 2022Mar 18, 2022

    • bookclub-islr

      Public
      Introduction to Statistical Learning Using R Book Club
      TeX
      •52•0•0•0•Updated Dec 14, 2021Dec 14, 2021

    • differential-expression-

      Public
      R
      •2•0•0•0•Updated Dec 13, 2021Dec 13, 2021

    • leafcutter-pipeline

      Public
      Differential splicing and visualisation pipeline for the Raj lab
      Python
      •6•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • unc13a_cryptic_splicing

      Public
      Figures for UNC13A paper
      paperrna-seq-analysis
      paperrna-seq-analysis
      R
      •1•4•0•0•Updated Oct 1, 2021Oct 1, 2021

    • pipeline_iclip

      Public
      Shell
      •1•3•0•0•Updated May 10, 2021May 10, 2021

    • tectools_pipeline

      Public
      snakemake pipeline to run tectools
      Python
      •0•0•0•0•Updated Feb 22, 2021Feb 22, 2021

    • PAQR_KAPAC

      Public
      scripts, pipelines and documentation to run PAQR and KAPAC; KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes; PAQR enabl…
      Python
      •
      GNU General Public License v2.0
      •4•0•0•0•Updated Nov 11, 2020Nov 11, 2020

    • downloading_from_sra

      Public
      Simple code for downloading from SRA in a parallel manner
      Python
      •0•0•0•0•Updated Nov 5, 2020Nov 5, 2020

    • MicroExonator

      Public
      Snakemake pipeline for microexon discovery and quantification
      Python
      •8•0•0•0•Updated Sep 21, 2020Sep 21, 2020

    • paqr_annotations

      Public
      Snakemake workflow to generate annotation files for PAQR
      Python
      •0•2•0•0•Updated Jun 18, 2020Jun 18, 2020

    • GeneStructureTools

      Public
      R
      •
      Other
      •3•0•0•0•Updated Jun 17, 2020Jun 17, 2020
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