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    21 repositories

    • tdp43-apa

      Public
      Code for TDP-43 APA manuscript
      Jupyter Notebook
      •1•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • SpliceNouveau

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 13, 2024Aug 13, 2024

    • QAPA_snakemake

      Public
      Snakemake pipeline to run QAPA and perform differential polyA site usage analysis
      Python
      •
      MIT License
      •0•1•4•0•Updated Jul 31, 2024Jul 31, 2024

    • rna_seq_snakemake

      Public
      Snakemake Pipeline For RNA-Seq in UCL Cluster
      Python
      •4•9•9•1•Updated May 24, 2024May 24, 2024

    • rna_seq_single_steps

      Public
      Snakemake pipelines for common bioinformatics tasks
      Python
      •1•0•1•0•Updated May 13, 2024May 13, 2024

    • 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•13•0•Updated Jan 19, 2024Jan 19, 2024

    • splicing

      Public
      Snakemake pipeline for running MAJIQ
      R
      •6•19•3•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•1•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
      •50•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
      •5•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • unc13a_cryptic_splicing

      Public
      Figures for UNC13A paper
      rna-seq-analysispaper
      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 enables the quantification of poly(A) site usage from standard RNA-seq data
      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