biomystery

django_highchart_demo

ROSE_young_lab

Epigen_LIMS_DOC

Documentation for using Epigen LIMS

atacMotif

Motif analysis of atac peaks

bio-cwl-tools

CWL CommandLineTool descriptions for biology/life-sciences related applications

ceR

A R package for Illumina BaseSpace Correlation Engine (CE) API

common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Coronavirus_Portal

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

DESeq2

Differential gene expression analysis based on the negative binomial distribution

django-cart-demo

A Django app handling shopping cart

duration_decode_manuscript

Code and Data for Gene Regulatory Strategies paper.

epigen_ucsd_django

gdcdictionary

Data dictionary for the GDC

HiC_scripts

HiC processing scripts used in the center.

igvShiny

an htmlwidget version of igv, for RStudio and Shiny apps

islet_figs_motifs

ngs_test_dataset

peakApp

A shiny app to connect the correlation matrix and each scatter plots

setQC

single_cell

SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

SnapTools

snATAC_pipeline_scanpy_based

A single-cell ATAC pipeline based on scanpy and clustering on most variable genomic bins. Originated from Josh@Kyle's lab.

tcell_project

RNA-seq analysis for cRel paper

TLR4_signaling_model

Code and data for TRL4 signaling paper.

TNF_regulation

Collabration with Andrew. Model's coding for TNF regulation in LPS, CpG and PIC

ulcerative_colitis

utility_epigen

workflows

Community maintained workflows & tools (with examples)