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1000genomes

scripts for processing 1000 Genomes and Geuvadis (RNA) data

basespacefastqdownload

Code to download fastq files to server directly from Illumina BaseSpace

bird-workflow

Repository to coordinate the effort to create a simplified workflow for running BIRD

ccgr_portal_cov_viz

Experiment Coverage libraries and application

ccgr_portal_data_loading

cegs-portal

CCGR Portal

chip-seq-pipeline2

chip-seq-qc-app

A MEAN web application that visualizes and displays ChIP-seq QC metrics for assessing and validating sample quality.

cov_viz

Generate data used by the CCGR Portal experiment coverage visualizer

cov_viz_ds

cov_viz_manifest

cradle

cwl-pipelines

CWL workflows developed in the Reddy lab to process genomics and functional genomics data

darryl_ggr_hdaci

encode4-duke-locusselect

encode_cart

Create and add items to ENCODE portal carts

exp_viz

Experiment coverage visualization filtering

fbi

Finding Broken Isoforms

gcrn

Repository for the Glucocorticoid Response Network project

gemberling-et-al-nmeth-a42509c

Collection of notebooks associated to the NMETH-A42509C manuscript by Gemberling et al.

genoverse

HTML5 scrollable genome browser

ggr-cwl-ipynb-gen

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

ggr-visual

Visualizations for data exploration of the GGR project

ggr_trackhub

Code to generate trackhub for GGR data visualization

grna_mrna_moi_exploration

Tools for exploring grna and mrna data

igvf-cwl

CWL tools and workflows for IGVF and more

jsom

Expect script for connecting to Jupyter notebooks on DASH/SOM-HPC

pmid_scraper

Code to scrape pubmed IDs from text files to enable generation of bibliographies

popstarr2

Pipeline for processing whole-genome Population STARR-seq data

programmingtips