ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

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

Python

65 +0

692 +4

286 +0

GitHub
RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

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

Python

78 +0

821 +6

287 +0

GitHub
rnaseq_tutorial by griffithlab

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

created at July 31, 2014, 6:58 p.m.

R

185 +0

1,303 +0

614 +0

GitHub
bioinformatics by ossu

microscope Path to a free self-taught education in Bioinformatics!

created at June 21, 2016, 11:11 p.m.

Unknown languages

356 +0

4,939 +19

835 +1

GitHub
Scribl by chmille4

HTML5 canvas genomic graphics library

created at Dec. 12, 2010, 9:18 p.m.

JavaScript

4 +0

76 +0

14 +0

GitHub
pileup.js by hammerlab

Interactive in-browser track viewer

created at Jan. 27, 2015, 8:36 p.m.

JavaScript

20 +0

271 +0

66 +0

GitHub
islandplot by lairdm

SVG based genome viewer written in javascript using D3

created at Nov. 6, 2013, 10:22 p.m.

JavaScript

5 +0

33 +0

27 +0

GitHub
dnaism by drio

Horizon chart js library for DNA data.

created at Jan. 6, 2014, 4:33 p.m.

CSS

8 +0

60 +0

6 +0

GitHub
Circleator by jonathancrabtree

Flexible circular visualization of genome-associated data with BioPerl and SVG.

created at Sept. 13, 2013, 8:19 p.m.

Perl

5 +0

45 +0

8 +0

GitHub
PyVCF by jamescasbon

A Variant Call Format reader for Python.

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

Python

31 +0

391 +0

198 +0

GitHub
samtools by samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

created at March 9, 2012, 2:49 a.m.

C

101 +0

1,532 +8

565 +0

GitHub
pysam by pysam-developers

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

created at Feb. 5, 2014, 8:38 p.m.

Cython

48 +0

743 +3

268 -1

GitHub
pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

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

Python

10 +0

436 +0

72 +0

GitHub
bedtools by arq5x

A powerful toolset for genome arithmetic.

created at Jan. 3, 2011, 2:43 a.m.

C++

20 +0

139 +0

87 +0

GitHub
pybedtools by daler

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

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

Python

17 +0

291 +1

101 +1

GitHub
cyvcf2 by brentp

cython + htslib == fast VCF and BCF processing

created at Aug. 12, 2015, 2:30 p.m.

Cython

7 +0

354 +1

70 +0

GitHub
cyvcf by arq5x

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

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

Python

6 +0

52 +0

13 +0

GitHub
bioservices by cokelaer

Access to Biological Web Services from Python.

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

Python

18 +0

271 +0

61 +0

GitHub
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.

Python

22 +0

350 +2

65 +0

GitHub
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.

Python

87 +0

971 +1

363 +0

GitHub