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pepatac
A modular, containerized pipeline for ATAC-seq data processingawesome-atac-analysis
Links to ATAC-seq analysis toolspypiper
Python toolkit for building restartable pipelinessimpleCache
Simplified R caching for reproducible big data projectsGenomicDistributions
Calculate and plot distributions of genomic rangesbulker
Manager for multi-container computing environmentsAIList
Augmented interval list (AIList): a novel data structure for efficient genomic interval searchunitar
Targets that span projects in RIGD
A high-performance search engine for large-scale genomic interval datasetsbedshift
Bedfile perturbation toolLOLAweb
An interactive Shiny web application for genomic interval enrichment analysis using LOLA.geniml
Genomic interval machine learningsciquill
Author academic documents in markdownCOCOA
Annotating epigenetic variation among samples with region sets in Rpeppro
A modular, containerized pipeline for PRO-seq data processingpararead
Simplifies parallel processing of DNA sequencing readsericscript
Chimeric transcript discoverycocoa_workshop_bioc2020
yacman
YAML configuration managerfolderfun
Manage distributed input and output data locations in R with folder functionsbds_hackathon
awesome-nascent-rna-analysis
A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysismarkmeld
A Python package for melding markdown content and YAML structured datahub.bulker.io
Bulker registryref_decoy
Decoy alignment sequencesbedbase
Aggregate, analyze, and serve genomic regions.shinyqueue
An R package that makes it easy to deploy shiny apps that process big dataloadr
Cleaner R workspacesregionset-embedding
GenomicDistributionsData
Data for GenomicDistributions R packagelogmuse
Small logging setup packagemkdocs-databio
Lab theme for mkdocsbdshack19
Coordinating the 2019 Biomedical Data Science Hackathon at UVAgtars
Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.bedms
tool for standardization of genomics/epigenomics metadatamm_templates
episb-provider
Describe a data provider for the Epigenome SwitchboardshinyBase
Base Docker image for Shiny-based web apps.pepatac_paper_data
Information on reproducing plots from the PEPATAC paperprojectInit
R project initializationdnameth_pipelines
PEP-compatible pipelines for DNA methylation data (RRBS, WGBS)FUSED
FUSion Error prone repair Detectionbedshift_analysis
schema.databio.org
Repository of JSON-schemaslucidoc
Automatic python documentation in markdown for mkdocsbedhost
API and UI for BEDbasefasta-id
bedbuncher
A pipeline for bedsetsepihet
Calculating epigenetic heterogeneityppqc
QC samples for PEPPRO pipelinebioterms
Content and Dockerfile for the bioterms.org sitepigmy
unitar_resources_demo
example-projects
tutorials on how to use the lab's toolsbedstat
pipeline for obtaining statistics about bed filesexample_analysis
bbconf
Configuration package for bedbase projectbedboss
Python pipeline for processing BED files for BEDbaseDESeqPackager
Generates a countTable from a PEP for DESeq analysisdockerfiles
Sheffield lab dockerfilesuniwig
COCOA_paper
henge
Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDsLove Open Source and this site? Check out how you can help us