Skip to content

@jknightlab jknightlab

All

    Repositories list

    30 repositories

    • Sample-identity-CHECK

      Public
      Shell
      •0•0•0•0•Updated Aug 7, 2026Aug 7, 2026

    • HIRV-TB_eQTL

      Public
      HTML
      •
      MIT License
      •1•0•0•0•Updated Jun 5, 2026Jun 5, 2026

    • MTOR-Genetics-Project

      Public
      R
      •1•1•0•0•Updated Feb 8, 2026Feb 8, 2026

    • TAPS-pipeline

      Public
      Codes for processing of methylation data generated using the TAPS method
      HTML
      •4•8•1•0•Updated Oct 9, 2025Oct 9, 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
      •7•10•1•0•Updated Jul 11, 2025Jul 11, 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

    • SepstratifieR

      Public
      Stratification of infectious disease patients by gene expression profile
      R
      •
      Other
      •4•8•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…
      0•0•0•0•Updated Sep 14, 2022Sep 14, 2022

    • AltHapAlignR

      Public
      R
      •0•6•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
      •4•5•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 n…
      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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.