databio/lucidoc databio/lucidoc

  • Stars
    star
    2
  • Language
    Python
  • Created over 5 years ago
  • Updated 11 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
databio/lucidoc
github

databio

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Automatic python documentation in markdown for mkdocs

More 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

bedhost

API and UI for BEDbase
TypeScript
2
star
47

fasta-id

JavaScript
1
star
48

bedbuncher

A pipeline for bedsets
Python
1
star
49

epihet

Calculating epigenetic heterogeneity
R
1
star
50

ppqc

QC samples for PEPPRO pipeline
1
star
51

bioterms

Content and Dockerfile for the bioterms.org site
HTML
1
star
52

pigmy

Python
1
star
53

unitar_resources_demo

R
1
star
54

example-projects

tutorials on how to use the lab's tools
1
star
55

bedstat

pipeline for obtaining statistics about bed files
Python
1
star
56

example_analysis

Makefile
1
star
57

bbconf

Configuration package for bedbase project
Python
1
star
58

bedboss

Python pipeline for processing BED files for BEDbase
Python
1
star
59

DESeqPackager

Generates a countTable from a PEP for DESeq analysis
R
1
star
60

dockerfiles

Sheffield lab dockerfiles
Shell
1
star
61

uniwig

C
1
star
62

COCOA_paper

R
1
star
63

henge

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