Explore @databio Open Source projects

Databio (@databio)

databio

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Location 🇺🇸 United States
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R
269

Jinja 366

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pepatac

A modular, containerized pipeline for ATAC-seq data processing

awesome-atac-analysis

Links to ATAC-seq analysis tools

pypiper

Python toolkit for building restartable pipelines

simpleCache

Simplified R caching for reproducible big data projects

GenomicDistributions

Calculate and plot distributions of genomic ranges

bulker

Manager for multi-container computing environments

Jupyter Notebook

AIList

Augmented interval list (AIList): a novel data structure for efficient genomic interval search

unitar

Targets that span projects in R

IGD

A high-performance search engine for large-scale genomic interval datasets

bedshift

Bedfile perturbation tool

LOLAweb

An interactive Shiny web application for genomic interval enrichment analysis using LOLA.

geniml

Genomic interval machine learning

sciquill

Author academic documents in markdown

MIRA

R package for Methylation-based Inference of Regulatory Activity

COCOA

Annotating epigenetic variation among samples with region sets in R

peppro

A modular, containerized pipeline for PRO-seq data processing

pararead

Simplifies parallel processing of DNA sequencing reads

ericscript

Chimeric transcript discovery

cocoa_workshop_bioc2020

yacman

YAML configuration manager

folderfun

Manage distributed input and output data locations in R with folder functions

bds_hackathon

Jupyter Notebook

awesome-nascent-rna-analysis

A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis

markmeld

A Python package for melding markdown content and YAML structured data

hub.bulker.io

Bulker registry

ref_decoy

Decoy alignment sequences

bedbase

Aggregate, analyze, and serve genomic regions.

Jupyter Notebook

shinyqueue

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

loadr

Cleaner R workspaces

regionset-embedding

Jupyter Notebook

GenomicDistributionsData

Data for GenomicDistributions R package

logmuse

Small logging setup package

mkdocs-databio

Lab theme for mkdocs

bdshack19

Coordinating the 2019 Biomedical Data Science Hackathon at UVA

Jupyter Notebook

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.

bedms

tool for standardization of genomics/epigenomics metadata

mm_templates

episb-provider

Describe a data provider for the Epigenome Switchboard

shinyBase

Base Docker image for Shiny-based web apps.

pepatac_paper_data

Information on reproducing plots from the PEPATAC paper

projectInit

R project initialization

dnameth_pipelines

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

FUSED

FUSion Error prone repair Detection

bedshift_analysis

schema.databio.org

Repository of JSON-schemas

lucidoc

Automatic python documentation in markdown for mkdocs

bedhost

API and UI for BEDbase

fasta-id

bedbuncher

A pipeline for bedsets

epihet

Calculating epigenetic heterogeneity

ppqc

QC samples for PEPPRO pipeline

bioterms

Content and Dockerfile for the bioterms.org site

pigmy

unitar_resources_demo

example-projects

tutorials on how to use the lab's tools

bedstat

pipeline for obtaining statistics about bed files

example_analysis

bbconf

Configuration package for bedbase project

bedboss

Python pipeline for processing BED files for BEDbase

DESeqPackager

Generates a countTable from a PEP for DESeq analysis

dockerfiles

Sheffield lab dockerfiles

uniwig

COCOA_paper

henge

Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs