Jack Humphrey's repositories
WGS-QC-Pipeline
A Snakemake pipeline for Quality Control of Whole Genome Sequencing data
ALS_SpinalCord_QTLs
Data Portal for NYGC ALS Spinal Cord
sqtlviztools
functions for sQTL visualisation
featuremaps
An R package for creating sophisticated plots of genomic intersections.
FTLD-TDP_analysis
"All code written for Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions"
FUS_intron_retention
Scripts written for the FUS NLS mutation comparison with FUS KO project
leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
fidelio
assessing spliceosome fidelity from RNA-seq junction reads
jackhump.github.io
Personal website
CMC_sQTLviz
Visualising LeafCutter sQTLs found in the CommonMind Consortium (CMC) brain dataset
editing-pipeline
A set of snakemake pipelines for doing RNA editing
gganatogram
Create anatograms using ggplot2
hnRNPK
All code written for hnRNPK manuscript
jacktools
a set of scripts for stupid things I have to do regularly. Mostly just a wrapper for BedTools.
learning_web_dev
Stuff I worked on for a Web Development course in June 2017
long_genes
where I keep my long genes scripts
New_beginnings_2.0
Important lab information for new starters!
opthalmology_work
Work for the UCL Institute of Opthalmology
pbmm2
A minimap2 frontend for PacBio native data formats
phd_thesis
My thesis - due for submission in November 2018
RNA-pipelines
A repo to contain various RNA-seq processing pipelines, to cut down how many different repos I have.
ROSMAP_sQTLviz
Visualising LeafCutter sQTLs found in the ROSMAP brain dataset
stanford_brain_work
Work in the Pritchard Lab at Stanford, CA
Two_TDP-43_Mutant_Mice
scripts written for Fratta et al "Endogenous TDP-43 mutant mice have novel gain of splicing function and ALS characteristics in vivo"