bakta by oschwengers

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

updated at April 28, 2024, 8:05 a.m.

14 +0

391 +5

42 +0

ChIP-seq-analysis by crazyhottommy

ChIP-seq analysis notes from Ming Tang

updated at April 28, 2024, 6 a.m.

65 +0

708 +6

290 +2

csvkit by wireservice

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

updated at April 28, 2024, 2:07 a.m.

130 -1

5,817 +5

601 +1

RNA-seq-analysis by crazyhottommy

RNAseq analysis notes from Ming Tang

updated at April 27, 2024, 11:05 a.m.

78 +0

839 +4

290 +0

hail by hail-is

Cloud-native genomic dataframes and batch computing

updated at April 26, 2024, 7:20 p.m.

55 +0

934 -2

235 +1

biopython by biopython

Official git repository for Biopython (originally converted from CVS)

updated at April 26, 2024, 7:53 a.m.

170 +0

4,169 +9

1,712 +1

pyfaidx by mdshw5

Efficient pythonic random access to fasta subsequences

updated at April 25, 2024, 2:33 p.m.

9 +0

440 +0

73 +0

pyensembl by openvax

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

updated at April 25, 2024, 1:45 p.m.

22 +0

352 +0

66 +0

cruzdb by brentp

python access to UCSC genomes database

updated at April 23, 2024, 8:01 p.m.

17 +0

134 +1

41 +0

gffutils by daler

GFF and GTF file manipulation and interconversion

updated at April 23, 2024, 3:10 p.m.

14 +0

267 +2

74 +0

redun by insitro

Yet another redundant workflow engine

updated at April 23, 2024, 9:54 a.m.

15 +0

486 +2

37 +0

bamsurgeon by adamewing

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

updated at April 23, 2024, 8:44 a.m.

15 +0

226 +1

83 +0

deepvariant by google

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

updated at April 22, 2024, 11:23 p.m.

160 +0

3,077 +1

695 +1

bcbio-nextgen by bcbio

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

updated at April 22, 2024, 11:12 a.m.

87 +0

973 -1

357 +0

poapy by ljdursi

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

updated at April 18, 2024, 7:29 p.m.

8 +0

68 +0

12 +0

ggd-cli by gogetdata

The command-line interface to GGD

updated at April 17, 2024, 12:59 p.m.

5 +0

42 +0

3 +0

pybedtools by daler

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

updated at April 11, 2024, 12:51 a.m.

17 +0

293 +0

103 +0

PyVCF by jamescasbon

A Variant Call Format reader for Python.

updated at April 10, 2024, 9:48 a.m.

31 +0

392 +0

199 +0

wormtable by wormtable

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

updated at April 5, 2024, 5:59 p.m.

6 +0

27 +0

5 +0

seqmagick by fhcrc

An imagemagick-like frontend to Biopython SeqIO

updated at March 31, 2024, 9:30 p.m.

12 +0

108 +0

22 +0