Repositories list

• IsoSLAM

  Public
  Python

  •

  MIT License

  •0•0•6•0•Updated Oct 25, 2024Oct 25, 2024

• pipeline_sylamer

  Public
  Shell

  •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

• Cancer3UIs

  Public
  Repository for code related to cancer 3UIs paper

  HTML

  •0•0•0•0•Updated Aug 13, 2024Aug 13, 2024

• pipeline_miRNA_seq

  Public
  miRseq and RNAseq pipeline analysis for Favour's data

  R

  •

  MIT License

  •0•0•0•0•Updated Jul 17, 2024Jul 17, 2024

• yonchev_et_al

  Public
  Code and genesets used in yonchev_et_al, 2023

  MIT License

  •0•0•0•0•Updated Jul 19, 2023Jul 19, 2023

• pipeline_motif_analysis

  Public
  de novo motif analysis with streme, homer and fire

  R

  •

  MIT License

  •0•1•0•0•Updated Mar 9, 2023Mar 9, 2023

• pipeline_salmonquant

  Public
  Python

  •1•0•0•1•Updated Oct 12, 2022Oct 12, 2022

• pipeline_slamdunk_umis

  Public
  R

  •1•0•0•0•Updated Jun 21, 2022Jun 21, 2022

• pipeline_utrons

  Public
  Python

  •2•0•0•0•Updated May 30, 2022May 30, 2022

• iCLIPlib

  Public
  Tools for dealing with iCLIP data

  Python

  •2•3•1•0•Updated Apr 4, 2022Apr 4, 2022

• pipeline_denovo_motifs

  Public
  Python

  •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021

• alvarez_et_al

  Public
  Code and other scripts for Alvarez-Beneyas et al 2020

  Jupyter Notebook

  •

  MIT License

  •2•1•0•0•Updated Jul 7, 2021Jul 7, 2021

• SpotDup

  Public
  A tool to predict the level of biological duplication in an RNA-Seq sample.

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated May 22, 2020May 22, 2020

• pipeline_germlinevariantcalls

  Public
  Pipeline for calling germline variants.

  Python

  •0•0•0•0•Updated Sep 3, 2019Sep 3, 2019

• Viphakone_et_al

  Public
  Project specific code used in Viphakone and Sudbery et al (2019), Mol Cell.

  Jupyter Notebook

  •0•0•0•0•Updated May 9, 2019May 9, 2019

• pipeline_apa

  Public
  Pipeline for the detection of alternative polyadenylation

  Python

  •0•0•0•0•Updated Feb 20, 2019Feb 20, 2019

• pipeline_metagenes

  Public
  A general purpose metagene pipeline for those occasions when a collaborators says "Can you just do me a quick metagene of...."

  Python

  •0•0•0•0•Updated Feb 6, 2019Feb 6, 2019

• pipeline_quasar

  Public
  JavaScript

  •0•0•0•0•Updated Jan 28, 2019Jan 28, 2019

• cgat

  Public
  CGAT - Computational Genomics Analysis Tools

  Python

  •

  Other

  •66•0•0•0•Updated Nov 29, 2018Nov 29, 2018

• pipeline_piq

  Public
  Python

  •0•0•0•0•Updated Oct 24, 2018Oct 24, 2018

• pipeline_tutorial

  Public
  Tutorial for using CGAT/ruffus pipelines

  Python

  •0•0•0•0•Updated Aug 27, 2018Aug 27, 2018

• CGATPipelines

  Public
  Collection of CGAT NGS Pipelines

  Python

  •

  MIT License

  •18•0•0•0•Updated Apr 2, 2018Apr 2, 2018

• pipeline_retained_introns

  Public
  Discover differentially retained introns using DEXSeq

  Python

  •0•1•0•0•Updated Mar 7, 2018Mar 7, 2018

• methylation_paper

  Public
  0•0•0•0•Updated Mar 1, 2018Mar 1, 2018

• utrons

  Public
  Python

  •0•0•0•0•Updated Oct 10, 2016Oct 10, 2016

• pipeline_capt_c_perl

  Public
  Pipeline to run the capture c perl scripts on reads

  Python

  •0•0•0•0•Updated Feb 17, 2016Feb 17, 2016

• project_bash_scripts

  Public
  Shell

  •0•0•0•0•Updated Feb 10, 2016Feb 10, 2016

• Capture_C_Perl_Scripts

  Public
  Scripts to analyze Capture C data in Perl

  Perl

  •0•2•0•0•Updated Feb 2, 2016Feb 2, 2016

• Capture_C

  Public
  A quick and dirty pipeline for caputre-c analysis written in ruffus and python.

  Python

  •0•0•0•0•Updated Dec 4, 2015Dec 4, 2015

• CGATReport

  Public
  A report generator using sphinx.

  Python

  •

  Other

  •5•0•0•0•Updated Nov 26, 2015Nov 26, 2015