Pinned 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
Candles
Data + code examples used here: https://twitter.com/kate_ptrv/status/1332398737604431874?s=20
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
data202
Class notes, datasets, project details, other information from DATA-202, Information Systems & Data Management, Fall 2020.
escape
Easy single cell analysis platform for enrichment
proj-Westra-data202
Walking through the analysis and a figure from a Nature Genetics article, replicating the lab's findings that mutations in genes are enriched based on specific exposures. || Data 202 Final Project, Fall 2020.
sbatchtools
sbatchtools is a suite of shell scripts to automate slurm submissions (based on www.github.com/LeeLMarshall/qsubtools)
kew24's Repositories
kew24/ALS_SpinalCord_QTLs
Data Portal for NYGC ALS Spinal Cord
kew24/biscuit
BISulfite-seq CUI Toolkit
kew24/Biscuit_Snakemake_Workflow
Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit
kew24/biscuiteer
tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output
kew24/ExpansionHunter
A tool for estimating repeat sizes
kew24/sbatchtools
sbatchtools is a suite of shell scripts to automate slurm submissions (based on www.github.com/LeeLMarshall/qsubtools)
kew24/gatk-sv
A structural variation pipeline for short-read sequencing
kew24/geneimpacts
prioritize effects of variant annotations from VEP, SnpEff, et al.
kew24/ggpackets
Cleaner composition of ggplot layers
kew24/glmmSeq
Gene-level general linear mixed model
kew24/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
kew24/MI-COVID-Viz
Create a visual of Michigan Covid Cases
kew24/miniwdl
Workflow Description Language developer tools & local runner
kew24/pathExplore
Gene Set Enrichment Clustering Plots
kew24/pbsPretty
colorful, descriptive alternatives to pbsnodes and qstat
kew24/qsubtools
kew24/r4ds
R for data science: a book
kew24/rnaseq_workflow
snakemake workflow for bulk RNA-seq workflow using STAR-edgeR
kew24/sc-type
kew24/scCustomize
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
kew24/scDblFinder
Methods for detecting doublets in single-cell sequencing data
kew24/scGate
marker-based purification of cell types from single-cell RNA-seq datasets
kew24/scRNA-seq_online
kew24/seurat
R toolkit for single cell genomics
kew24/Single-Cell-RNA-Boost
kew24/speckle
R package for analysing single cell data
kew24/STAR
RNA-seq aligner
kew24/str-analysis
Scripts and utilities related to analyzing short tandem repeats (STRs).
kew24/STRling
Detect novel (and reference) STR expansions from short-read data
kew24/warp
WDL Analysis Research Pipelines