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archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

bosc-2016-ggr-cwl

Abstract for BOSC 2016

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

crispr-jamboree

2nd IGVF CRISPR-JAMBOREE (Feb 2024)

cwl-draft3-to-v1-parser

Upgrade CWL workflows and CLT from draft-3 to v1.0 syntax

cwltool

Common Workflow Language reference implementation

docker-hubutils

UCSC hub and bed utils in Docker

encoded

Metadata database for ENCODE project

encvaldata

fungidomdb

Database for fungal protein domain information

geoparse

Python library to access Gene Expression Omnibus Database (GEO)

get-hic

get-hic-docker

ggr-cwl

CWL tools and workflows for GGR

ggr-cwl-ipynb-gen

Jupyter notebook generator to download and execute the processing files for GGR related datasets

ggr-docker

Docker images for containerizing GGR analyses

ggr-visual

Visualizations for data exploration of the GGR project

juicebox

Software for visualizing data from Hi-C and other proximity mapping experiments

lab-meeting-20180315

Repository for lab meeting 2018/03/15

macs

MACS -- Model-based Analysis of ChIP-Seq

majiq-voila-elife

Repository to support the reproducibility of the results contained in Vaquero et al. manuscript published in eLife

pipeline_perturbseq_like

pyencoded-tools

reddylab-disk-usage

Summarize reddylab disk usage in HARDAC

time-series-cwl

CWL pipeline to create the necessary files to create the visualizations offered in the time-series-viewers package (https://github.com/alexbarrera/time-series-viewers)

time-series-viewers

Visualize time series sequencing data

tinyatlas

A tiny cell atlas for commonly sequenced organisms.

toil

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

velocyto.r

RNA velocity estimation in R

workflows

Community maintained workflows & tools (with examples)