Repositories list

• TAPS-pipeline

  Public
  Codes for processing of methylation data generated using the TAPS method

  Shell

  •0•4•0•0•Updated Jul 16, 2025Jul 16, 2025

• Enhancer-RNA

  Public
  Shell

  •

  MIT License

  •1•0•0•0•Updated Jul 14, 2025Jul 14, 2025

• eqtl-intro

  Public
  An introductory course to eQTL analysis.

  HTML

  •

  MIT License

  •6•9•1•0•Updated Jul 11, 2025Jul 11, 2025

• MTOR-Genetics-Project

  Public
  R

  •1•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• DESeq2-Tutorial

  Public
  HTML

  •1•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• ONT-methylation-pipeline

  Public
  Codes used for analysing sequencing data and modified base information derived using ONT

  Shell

  •2•1•0•0•Updated Jul 19, 2024Jul 19, 2024

• ICeCAP

  Public
  Fork of Gabriele's ICeCAP pipeline for reference in the jknightlab GitHub

  C

  •1•0•0•0•Updated Mar 22, 2023Mar 22, 2023

• Sample-identity-CHECK

  Public
  Shell

  •0•0•0•0•Updated Nov 2, 2022Nov 2, 2022

• SepstratifieR

  Public
  Stratification of infectious disease patients by gene expression profile

  R

  •

  Other

  •4•6•0•0•Updated Sep 14, 2022Sep 14, 2022

• SepstratifieR-paper_Sci-Trans-Med_2022

  Public
  This repository contains all the codes associated with the paper "An immune dysfunction score for stratification of patients with acute infection based on whole blood gene expression" by Cano-Gamez et al.

  0•0•0•0•Updated Sep 14, 2022Sep 14, 2022

• AltHapAlignR

  Public
  R

  •0•5•1•0•Updated Sep 11, 2019Sep 11, 2019

• Abu-Dhabi

  Public
  Abu Dhabi population genetics and T2D/metformin RNAseq

  R

  •0•1•0•0•Updated Dec 19, 2018Dec 19, 2018

• latex-thesis

  Public
  TeX

  •2•3•0•1•Updated Oct 22, 2018Oct 22, 2018

• GitHub_and_Rmd_Introduction

  Public
  An introduction to using git and R markdown to document projects

  HTML

  •1•1•0•0•Updated Feb 8, 2017Feb 8, 2017

• AD_git

  Public
  upload AD docs

  0•0•0•0•Updated Nov 10, 2016Nov 10, 2016

• ATACseq_pipeline

  Public
  Shell

  •2•4•0•0•Updated Sep 28, 2016Sep 28, 2016

• HTSeq

  Public
  High throughput / next generation sequencing pipeline

  1•0•0•0•Updated Sep 28, 2016Sep 28, 2016

• heatshock

  Public
  Analysis of the transcriptional response to heat shock in LCLs

  TeX

  •0•1•0•0•Updated Sep 1, 2016Sep 1, 2016

• hussein_rnaseq

  Public
  R

  •0•0•0•0•Updated Jul 25, 2016Jul 25, 2016

• mirna_pipeline

  Public
  bioinformatics pipeline to analyze micro RNA sequencing data

  R

  •4•4•0•0•Updated Jun 24, 2016Jun 24, 2016

• RNA-Seq_course

  Public
  4•2•0•0•Updated May 26, 2016May 26, 2016

• impute-tools

  Public
  Scripts to facilitate imputation of genotypes and subsequent QC.

  Perl

  •

  MIT License

  •5•4•0•0•Updated Nov 19, 2015Nov 19, 2015

• mePipe

  Public
  Functions to support running of Matrix-eQTL analysis pipeline. This includes support for adding principle components as covariates and determining the optimal number of principal components to include.

  R

  •

  MIT License

  •1•2•1•0•Updated Sep 8, 2015Sep 8, 2015

• neut-blueprint

  Public
  Blueprint analysis of Neutrophil eQTL data

  MIT License

  •0•0•0•0•Updated Jul 7, 2015Jul 7, 2015

• analysis-with-docker

  Public
  Slides discussing how to use Docker for data analyses.

  JavaScript

  •

  Other

  •0•0•0•0•Updated May 19, 2015May 19, 2015

• git-intro

  Public
  A brief introduction to git and GitHub.

  CSS

  •0•0•0•0•Updated Mar 27, 2015Mar 27, 2015

• genotype-tools

  Public
  Scripts to facilitate processing of genotyping data.

  Perl

  •

  MIT License

  •1•1•0•0•Updated Feb 2, 2015Feb 2, 2015

• influenza

  Public
  GNU General Public License v2.0

  •0•0•0•0•Updated Jan 6, 2015Jan 6, 2015

• eQTL-plots

  Public
  0•0•0•0•Updated Dec 8, 2014Dec 8, 2014