databio Goto Github PK
Name: Databio
Type: Organization
Bio: Solving problems in computational biology
Location: University of Virginia
Blog: https://databio.org
Databio's Projects
ailist
Augmented interval list (AIList): a novel data structure for efficient genomic interval search
atac_ebna2
Example ATAC-seq project
awesome-atac-analysis
Links to ATAC-seq analysis tools
awesome-nascent-rna-analysis
A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis
bbconf
Configuration package for bedbase project
bds_hackathon
bdshack19
Coordinating the 2019 Biomedical Data Science Hackathon at UVA
bdshack2023
bedbase
Aggregate, analyze, and serve genomic regions.
bedboss
Python pipeline for processing BED files for BEDbase
bedbuncher
A pipeline for bedsets
bedhost
API and UI for BEDbase
bedhost-ui
bedlifter
bedbase supplemental pipeline to liftOver files
bedmaker
pipeline to convert bigWig, bedGraph and other file types into BED format
bedms
tool for standardization of genomics/epigenomics metadata
bedshift
Bedfile perturbation tool
bedshift_analysis
bedstat
pipeline for obtaining statistics about bed files
bioterms
Content and Dockerfile for the bioterms.org site
bsread
Parses bisulfite sequencing data
bulker
Manager for multi-container computing environments
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.
cocoa
Annotating epigenetic variation among samples with region sets in R
cocoa_paper
cocoa_workshop_bioc2020
databio_genomes
A list of lab genome assets to be built with refgenie
deseqpackager
Generates a countTable from a PEP for DESeq analysis
dnameth_pipelines
PEP-compatible pipelines for DNA methylation data (RRBS, WGBS)
dockerfiles
Sheffield lab dockerfiles
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