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
FTLD-TDP_analysis
"All code written for Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions"
featuremaps
An R package for creating sophisticated plots of genomic intersections.
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
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
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"