Databio

Solving problems in computational biology

University of Virginia

Pinned Repositories

AIList
Augmented interval list (AIList): a novel data structure for efficient genomic interval search
Language:C21 9 175
awesome-atac-analysis
Links to ATAC-seq analysis tools
49 20 06
bulker
Manager for multi-container computing environments
Language:Jupyter Notebook24 16 722
COCOA
Annotating epigenetic variation among samples with region sets in R
Language:R10 11 360
GenomicDistributions
Calculate and plot distributions of genomic ranges
Language:R25 16 9410
LOLAweb
An interactive Shiny web application for genomic interval enrichment analysis using LOLA.
Language:R16 5 852
MIRA
R package for Methylation-based Inference of Regulatory Activity
Language:R11 17 101
pepatac
A modular, containerized pipeline for ATAC-seq data processing
Language:R54 21 23714
pypiper
Python toolkit for building restartable pipelines
Language:Python45 16 1689
simpleCache
Simplified R caching for reproducible big data projects
Language:R34 20 256

Databio's Repositories

databio/pepatac
A modular, containerized pipeline for ATAC-seq data processing
Language:R54 21 23714
databio/pypiper
Python toolkit for building restartable pipelines
Language:Python45 16 1689
databio/GenomicDistributions
Calculate and plot distributions of genomic ranges
Language:R25 16 9410
databio/bulker
Manager for multi-container computing environments
Language:Jupyter Notebook24 16 722
databio/geniml
Genomic interval machine learning
Language:Python16 2 50
databio/sciquill
Author academic documents in markdown
Language:TeX12 8 85
databio/COCOA
Annotating epigenetic variation among samples with region sets in R
Language:R10 11 360
databio/yacman
YAML configuration manager
Language:Python7 16 342
databio/hub.bulker.io
Bulker registry
Language:HTML5 15 61
databio/markmeld
A Python package for melding markdown content and YAML structured data
Language:Python5 2 182
databio/bedbase
Aggregate, analyze, and serve genomic regions.
Language:Jupyter Notebook4 7 46
databio/bedms
tool for standardization of genomics/epigenomics metadata
Language:Python3
databio/gtars
Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package.
Language:Rust3 7 161
databio/logmuse
Small logging setup package
Language:Python3 9 171
databio/mm_templates
Language:Jinja3 3 0
databio/bedhost
API and UI for BEDbase
Language:TypeScript2
databio/lucidoc
Automatic python documentation in markdown for mkdocs
Language:Python2 9 351
databio/schema.databio.org
Repository of JSON-schemas
Language:JavaScript2 17 51
databio/bbconf
Configuration package for bedbase project
Language:Python1 11 302
databio/bedboss
Python pipeline for processing BED files for BEDbase
Language:Python1 2 48
databio/bedbuncher
A pipeline for bedsets
Language:Python1 9 18
databio/bedstat
pipeline for obtaining statistics about bed files
Language:Python1 17 241
databio/dockerfiles
Sheffield lab dockerfiles
Language:Shell1 18 2
databio/fasta-id
Language:JavaScript1 1 0
databio/henge
Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs
Language:Python1 8 1
databio/uniwig
Language:C1 19 7
databio/bedhost-ui
Language:JavaScript0 7 151
databio/bedmaker
pipeline to convert bigWig, bedGraph and other file types into BED format
Language:Python13 141
databio/region2vec_eval
Language:Jupyter Notebook
databio/rust-gc-count
A tool for generating wiggle files of GC from DNA written in Rust.