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pepatac
A modular, containerized pipeline for ATAC-seq data processingawesome-atac-analysis
Links to ATAC-seq analysis toolssimpleCache
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 markdownMIRA
R package for Methylation-based Inference of Regulatory ActivityCOCOA
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