Databio (@databio)
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Top repositories

1

pepatac

A modular, containerized pipeline for ATAC-seq data processing
R
53
star
2

awesome-atac-analysis

Links to ATAC-seq analysis tools
47
star
3

pypiper

Python toolkit for building restartable pipelines
Python
45
star
4

simpleCache

Simplified R caching for reproducible big data projects
R
34
star
5

GenomicDistributions

Calculate and plot distributions of genomic ranges
R
25
star
6

bulker

Manager for multi-container computing environments
Jupyter Notebook
24
star
7

AIList

Augmented interval list (AIList): a novel data structure for efficient genomic interval search
C
19
star
8

unitar

Targets that span projects in R
R
17
star
9

IGD

A high-performance search engine for large-scale genomic interval datasets
C
17
star
10

bedshift

Bedfile perturbation tool
Python
16
star
11

LOLAweb

An interactive Shiny web application for genomic interval enrichment analysis using LOLA.
R
16
star
12

geniml

Genomic interval machine learning
Python
15
star
13

sciquill

Author academic documents in markdown
TeX
12
star
14

MIRA

R package for Methylation-based Inference of Regulatory Activity
R
11
star
15

COCOA

Annotating epigenetic variation among samples with region sets in R
R
10
star
16

peppro

A modular, containerized pipeline for PRO-seq data processing
Python
9
star
17

pararead

Simplifies parallel processing of DNA sequencing reads
Python
9
star
18

ericscript

Chimeric transcript discovery
R
8
star
19

cocoa_workshop_bioc2020

Dockerfile
7
star
20

yacman

YAML configuration manager
Python
7
star
21

folderfun

Manage distributed input and output data locations in R with folder functions
R
7
star
22

bds_hackathon

Jupyter Notebook
6
star
23

awesome-nascent-rna-analysis

A collection of tools, pipelines, and guides for performing nascent RNA sequencing analysis
6
star
24

markmeld

A Python package for melding markdown content and YAML structured data
Python
5
star
25

hub.bulker.io

Bulker registry
HTML
5
star
26

ref_decoy

Decoy alignment sequences
5
star
27

bedbase

Aggregate, analyze, and serve genomic regions.
Jupyter Notebook
4
star
28

shinyqueue

An R package that makes it easy to deploy shiny apps that process big data
R
4
star
29

loadr

Cleaner R workspaces
R
3
star
30

regionset-embedding

Jupyter Notebook
3
star
31

GenomicDistributionsData

Data for GenomicDistributions R package
R
3
star
32

logmuse

Small logging setup package
Python
3
star
33

mkdocs-databio

Lab theme for mkdocs
JavaScript
3
star
34

bdshack19

Coordinating the 2019 Biomedical Data Science Hackathon at UVA
Jupyter Notebook
3
star
35

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.
Rust
3
star
36

bedms

tool for standardization of genomics/epigenomics metadata
Python
3
star
37

mm_templates

Jinja
3
star
38

episb-provider

Describe a data provider for the Epigenome Switchboard
Scala
2
star
39

shinyBase

Base Docker image for Shiny-based web apps.
Dockerfile
2
star
40

pepatac_paper_data

Information on reproducing plots from the PEPATAC paper
R
2
star
41

projectInit

R project initialization
R
2
star
42

dnameth_pipelines

PEP-compatible pipelines for DNA methylation data (RRBS, WGBS)
Python
2
star
43

FUSED

FUSion Error prone repair Detection
R
2
star
44

bedshift_analysis

Python
2
star
45

schema.databio.org

Repository of JSON-schemas
JavaScript
2
star
46

lucidoc

Automatic python documentation in markdown for mkdocs
Python
2
star
47

bedhost

API and UI for BEDbase
TypeScript
2
star
48

fasta-id

JavaScript
1
star
49

bedbuncher

A pipeline for bedsets
Python
1
star
50

epihet

Calculating epigenetic heterogeneity
R
1
star
51

ppqc

QC samples for PEPPRO pipeline
1
star
52

bioterms

Content and Dockerfile for the bioterms.org site
HTML
1
star
53

pigmy

Python
1
star
54

unitar_resources_demo

R
1
star
55

example-projects

tutorials on how to use the lab's tools
1
star
56

bedstat

pipeline for obtaining statistics about bed files
Python
1
star
57

example_analysis

Makefile
1
star
58

bbconf

Configuration package for bedbase project
Python
1
star
59

bedboss

Python pipeline for processing BED files for BEDbase
Python
1
star
60

DESeqPackager

Generates a countTable from a PEP for DESeq analysis
R
1
star
61

dockerfiles

Sheffield lab dockerfiles
Shell
1
star
62

uniwig

C
1
star
63

COCOA_paper

R
1
star
64

henge

Keeper of DRUIDs: a Python interface to Decomposable Recursive UIDs
Python
1
star