merckey Goto Github PK

cellassign-paper

Analysis pipelines for cellassign manuscript

cerebro-paper

chip-seq

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

cnvworkflow_meetup

2018 NYC R/Bioconductor Meetup Presentation

cnvworkflow_terra_wdl

CNV analysis workflows for Terra workspace

colonicepithelium

colonmesenchymescrnaseq

Analysis of 10x scRNA-Seq of human and murine colonic stromal cell transcriptomic data in health in IBD

complexheatmap

make complex heatmaps as well as self define annotation graphics

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

covgen

Creates a target specific exome_full192.coverage.txt file required by MutSig

covid19-scatac-seq

covid_balf

R script for the covid balf data analysis

cruk-summer-school-2020

Web-site for the 2020 CRUK CC Bioinformatics Summer School (Held virtually)

cruk_ci_summer_school_scrnaseq_2021

Single Cell Materials for 2021 CRUK Summer School

csf_aging

Single cell transcriptomics reveals cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment

deciphermutationalsignatures

Deciphering mutational signatures with alternative algorithms

denovomutpipeline

a series of scripts for analyzing de novo mutations in TCGA data

docker-dropbox

:whale: Dropbox in a Docker image. This works.

docker-dropbox-app

:whale: A docker container for dropbox by App

doublet-detection-benchmark

Benchmarking computational doublet-detection methods for single-cell RNA sequencing data

dropkick-manuscript

Scripts and notebooks for reproducing analysis in the 2020 dropkick manuscript.

edf4j

Java parser for edf format

excelerate-scrnaseq

Single RNA-seq data analysis with R (Finland, May, 2019)

f1000_workflow

facets_snakemake

Pipeline for running the FACETS copy number caller using Snakemake

fibernmicrobiome

Data, scripts and outputs for the paper "Gut microbiome variation modulates the effects of dietary fiber on host metabolism"

gatk

GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses

gatk-1

Official code repository for GATK versions 4 and up

gatk-docker

Docker source file for duplexa/gatk_env:v1 on hub.docker.com