kew24's repositories
ALS_SpinalCord_QTLs
Data Portal for NYGC ALS Spinal Cord
biscuit
BISulfite-seq CUI Toolkit
Biscuit_Snakemake_Workflow
Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit
biscuiteer
tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output
ExpansionHunter
A tool for estimating repeat sizes
sbatchtools
sbatchtools is a suite of shell scripts to automate slurm submissions (based on www.github.com/LeeLMarshall/qsubtools)
gatk-sv
A structural variation pipeline for short-read sequencing
geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
ggpackets
Cleaner composition of ggplot layers
glmmSeq
Gene-level general linear mixed model
hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
MI-COVID-Viz
Create a visual of Michigan Covid Cases
miniwdl
Workflow Description Language developer tools & local runner
pathExplore
Gene Set Enrichment Clustering Plots
pbsPretty
colorful, descriptive alternatives to pbsnodes and qstat
r4ds
R for data science: a book
rnaseq_workflow
snakemake workflow for bulk RNA-seq workflow using STAR-edgeR
scCustomize
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
scDblFinder
Methods for detecting doublets in single-cell sequencing data
scGate
marker-based purification of cell types from single-cell RNA-seq datasets
seurat
R toolkit for single cell genomics
speckle
R package for analysing single cell data
STAR
RNA-seq aligner
str-analysis
Scripts and utilities related to analyzing short tandem repeats (STRs).
STRling
Detect novel (and reference) STR expansions from short-read data
warp
WDL Analysis Research Pipelines