Projects in Awesome Lists by databio

Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.

Last synced: 12 Apr 2025

https://github.com/databio/ref_decoy

Decoy alignment sequences

Last synced: 10 Mar 2026

https://github.com/databio/bedbase

Aggregate, analyze, and serve genomic regions.

genomic-intervals

Last synced: 12 Apr 2025

https://github.com/databio/regionset-embedding

Last synced: 02 Jul 2025

https://github.com/databio/shinyqueue

An R package that makes it easy to deploy shiny apps that process big data

Last synced: 19 Apr 2026

https://github.com/databio/logmuse

Small logging setup package

Last synced: 12 Apr 2025

https://github.com/databio/bdshack19

Coordinating the 2019 Biomedical Data Science Hackathon at UVA

Last synced: 06 Oct 2025

https://github.com/databio/mm_templates

Last synced: 04 Mar 2026

https://github.com/databio/loadr

Cleaner R workspaces

Last synced: 03 Aug 2025

https://github.com/databio/bedms

Tool for standardization of genomics/epigenomics metadata

genetics genomic-intervals metadata

Last synced: 10 Mar 2026

https://github.com/databio/genomicdistributionsdata

Data for GenomicDistributions R package

Last synced: 05 Feb 2026

https://github.com/databio/mkdocs-databio

Lab theme for mkdocs

Last synced: 03 Mar 2026

https://github.com/databio/bedshift_analysis

Last synced: 31 May 2026

https://github.com/databio/henge

Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs

Last synced: 26 May 2026

https://github.com/databio/bedboss

Python pipeline for processing BED files for BEDbase

bed-files bed-format genomic-intervals geo

Last synced: 27 Feb 2026

https://github.com/databio/dnameth_pipelines

PEP-compatible pipelines for DNA methylation data (RRBS, WGBS)

Last synced: 06 Jun 2026

https://github.com/databio/fused

FUSion Error prone repair Detection

Last synced: 18 Apr 2026

https://github.com/databio/shinybase

Base Docker image for Shiny-based web apps.

docker react shiny

Last synced: 01 May 2026

https://github.com/databio/pepatac_paper_data

Information on reproducing plots from the PEPATAC paper

Last synced: 29 May 2026

https://github.com/databio/schema.databio.org

Repository of JSON-schemas

Last synced: 03 Feb 2026

https://github.com/databio/episb-provider

Describe a data provider for the Epigenome Switchboard

Last synced: 15 Jun 2025

https://github.com/databio/projectInit

R project initialization

Last synced: 30 Jul 2025

https://github.com/databio/projectinit

R project initialization

Last synced: 08 Oct 2025

https://github.com/databio/bedhost

API and UI for BEDbase

bed bioinformatics fastapi genomic-intervals genomics rest-api server

Last synced: 21 Jan 2026

https://github.com/databio/lucidoc

Automatic python documentation in markdown for mkdocs

Last synced: 11 Feb 2026

https://github.com/databio/fasta-id

Last synced: 09 Oct 2025

https://github.com/databio/unitar_resources_demo

Last synced: 11 Jul 2025

https://github.com/databio/deseqpackager

Generates a countTable from a PEP for DESeq analysis

Last synced: 20 Jul 2025

https://github.com/databio/epihet

Calculating epigenetic heterogeneity

Last synced: 02 Aug 2025

https://github.com/databio/ppqc

QC samples for PEPPRO pipeline

Last synced: 19 Mar 2026

https://github.com/databio/cocoa_paper

Last synced: 19 Apr 2026

https://github.com/databio/dockerfiles

Sheffield lab dockerfiles

Last synced: 15 Jul 2025

https://github.com/databio/example_analysis

Last synced: 19 Mar 2026

https://github.com/databio/uniwig

Last synced: 23 Jul 2025

https://github.com/databio/bioterms

Content and Dockerfile for the bioterms.org site

Last synced: 05 Mar 2026

https://github.com/databio/example-projects

tutorials on how to use the lab's tools

Last synced: 07 Feb 2026

https://github.com/databio/pigmy

Last synced: 03 Sep 2025

https://github.com/databio/git-and-github-fundamentals-nsheff

git-and-github-fundamentals-nsheff created by GitHub Classroom

Last synced: 07 Mar 2026

https://github.com/databio/seqcosts

Last synced: 19 Mar 2026

https://github.com/databio/scexprviz

A shiny app to visualize gene expression data from clustered cells

Last synced: 21 May 2026

https://github.com/databio/bedlifter

bedbase supplemental pipeline to liftOver files

Last synced: 21 Apr 2026

https://github.com/databio/paqc

PEPATAC qc project

Last synced: 07 Mar 2026

https://github.com/databio/databio_genomes

A list of lab genome assets to be built with refgenie

Last synced: 09 Mar 2026

https://github.com/databio/hichip-pipeline

Last synced: 05 Mar 2025

https://github.com/databio/example_python_cli

A skeleton python package demonstrating how to create a python CLI tool using logmuse.

Last synced: 28 Jul 2025

https://github.com/databio/methylation_age_prediction

Last synced: 06 Mar 2026

https://github.com/databio/refgetstore-node-demo

Lightweight Node.js refget + seqcol API server backed by RefgetStore

Last synced: 20 Jun 2026

https://github.com/databio/pytorch_tutorial

A concise introudction to Pytorch

Last synced: 19 Apr 2026

https://github.com/databio/bsread

Parses bisulfite sequencing data

Last synced: 11 Jun 2026

https://github.com/databio/region2vec_eval

Last synced: 19 Apr 2026

https://github.com/databio/bbconf

Configuration package for bedbase project

config-management genomic-intervals python-api

Last synced: 01 Feb 2026

https://github.com/databio/sciquill_old

The new mediabuilder

Last synced: 26 Feb 2026

https://github.com/databio/bdshack2023

Last synced: 20 Apr 2026

https://github.com/databio/atac_ebna2

Example ATAC-seq project

Last synced: 10 Feb 2026

https://github.com/databio/lolaews-db

PEP for Ewing Sarcoma LOLA database

Last synced: 06 Mar 2026

https://github.com/databio/lolahema_pep

Portable Encapsulated Project for the LOLAHema database.

Last synced: 19 Apr 2026

https://github.com/databio/episb-hub

Web UI/API for the Epigenome Switchboard Project

Last synced: 19 Mar 2026

https://github.com/databio/sciquill_paper_example

Last synced: 19 Mar 2026

https://github.com/databio/cellspecificopenchromatin

Preprocessing scripts to create a matrix, where columns are different cell types, raws are open chromatin regions and values are signal ATAC-seq signal intensities.

Last synced: 20 Apr 2026