bcbio-nextgen by bcbio

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

created at Feb. 6, 2013, 11:14 a.m.

87 +0

974 +1

357 +0

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

created at June 12, 2015, 9:42 p.m.

65 +0

702 +3

288 +0

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

created at Aug. 26, 2015, 7:37 p.m.

78 +0

835 +1

290 +1

PyVCF by jamescasbon

A Variant Call Format reader for Python.

created at Oct. 30, 2011, 4:52 p.m.

31 +0

392 +0

199 +1

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

created at Sept. 12, 2013, 7:02 p.m.

9 +0

440 +2

73 +1

pybedtools by daler

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

created at May 14, 2010, 9:09 p.m.

17 +0

293 +0

103 +0

cyvcf by arq5x

A fast Python library for VCF files leveraging Cython for speed.

created at April 12, 2012, 6:51 p.m.

6 +0

52 +0

13 +0

bioservices by cokelaer

Access to Biological Web Services from Python.

created at Aug. 28, 2014, 3:24 p.m.

18 +0

271 +0

61 +0

pyensembl by openvax

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

created at April 14, 2014, 3:23 p.m.

22 +0

352 +0

66 +0

cruzdb by brentp

python access to UCSC genomes database

created at Sept. 2, 2011, 3:36 p.m.

17 +0

133 +0

41 +0

bamsurgeon by adamewing

tools for adding mutations to existing .bam files, used for testing mutation callers

created at May 10, 2012, 10:18 p.m.

15 +0

225 +0

83 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

created at Oct. 12, 2011, 1:48 p.m.

14 +0

265 +1

74 +0

mergesam by DarwinAwardWinner

Automate common sam & bam conversions

created at Aug. 26, 2011, 2:19 p.m.

3 +0

6 +0

1 +0

bam-toolbox by AndersenLab

A bam toolbox

created at Oct. 28, 2015, 4:36 p.m.

10 +0

1 +0

1 +0

fastqp by mdshw5

Simple FASTQ quality assessment using Python

created at Sept. 23, 2013, 8:01 p.m.

6 +0

107 +0

14 +0

AfterQC by OpenGene

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

created at Aug. 4, 2015, 2:08 p.m.

20 +0

201 +0

51 +0

wormtable by wormtable

Write-once-read-many table for large datasets.

created at Oct. 27, 2012, 5:01 p.m.

6 +0

27 +0

5 +0

easy_qsub by shenwei356

Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.

created at March 9, 2015, 9:40 a.m.

3 +0

28 +0

8 +0

csvkit by wireservice

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

created at April 1, 2011, 3 a.m.

131 +0

5,812 +4

600 +0

hail by hail-is

Cloud-native genomic dataframes and batch computing

created at Oct. 27, 2015, 8:55 p.m.

55 +0

936 +2

234 -2