New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
11 months
30
18
60246
0
1
Parser of scientific names (...) !
Dmitry Mozzherin
4 months
10
5
33465
0
0
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
9 months
14
11
27659
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
5 days
16
4
21780
9
37
Http requests to entrez e-utilities (...)
Jared Ning
2 years
4
...
17733
0
0
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
4 weeks
13
1
17110
0
15
Webservice client library for intermine data-warehouses (...)
Alex Kalderimis
9 months
16333
Gadgets for bioinformatics (...)
Shintaro Katayama
10 months
...
14472
0
0
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
2 months
30
30
14187
0
9
Gff3 parser for big data (...) !
Pjotr Prins
20 months
6
2
14133
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
20 months
10
30
12100
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
10309
A biogem to submit jobs on a queue (...)
Francesco Strozzi
18 months
5
...
10198
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
3 months
7
5
9237
Very fast blast xml parser and library for (...) !
Pjotr Prins
14 months
9
...
8227
0
0
A fast parser for fastq files (...)
Francesco Strozzi
22 months
9
...
7939
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
22 months
6
4
7424
0
0
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
7033
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
7 weeks
8
20
6711
0
26
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
14 months
1
...
6701
0
6
Build genome output files (...) !
Michael Barton
8 months
...
6491
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
6292
0
0
Low memory sequence emitters (...)
Pjotr Prins
11 months
8
1
6078
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
4 years
5828
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
23 months
6
1
5796
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
10 months
6
...
5736
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
20 months
1
...
5709
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
16 months
2
...
5587
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
5562
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
5490
Ruby wrapper for sambamba tool (...)
Artem Tarasov
20 months
2
...
5289
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5182
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
8 months
7
3
5087
0
10
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
22 months
27
14
5024
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
10 months
5
...
4930
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
2 years
1
...
4816
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
7 months
13
3
4649
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
3 years
8
...
4270
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
3
...
4085
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
4
4018
0
0
A plugin that allows you to parse large (...)
robsyme
2 years
1
...
3915
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
20 months
2
...
3899
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
17 months
1
...
3722
Read and manipulate cd-hit clusters (...)
George Githinji
12 months
2
1
3291
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3214
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3182
0
0
Ruby binding for samtools tabix (...)
throwern
6 months
3
...
2949
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
20 months
2902
Bioinformatics triple-store support (...)
Pjotr Prins
23 months
4
1
2896
0
21
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
2839
0
0
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
21 months
1
1
2831
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
18 months
1
...
2810
0
0
Next-generation mapping of mutations (...)
Dan MacLean
16 months
2
...
2806
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
2 years
1
...
2678
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
23 months
1
...
2488
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2447
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
8 months
8
2
2404
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
23 months
1
...
2098
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
14 months
...
2048
A protparam compatible utility for BioRuby (...)
hryk
16 months
1
...
2042
0
6
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
17 months
2
...
1949
0
0
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
11 months
...
1927
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
8 months
1
...
1908
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
7 months
...
1751
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1673
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1655
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
2 years
1
1654
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1632
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1404
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
2 years
1
...
1402
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
2 years
...
1362
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
2 years
2
...
1351
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1339
0
0
One-line summary of your gem (...)
Toshiaki Katayama
2 years
1
...
1334
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
2 years
2
...
1304
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
23 months
3
...
1295
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1280
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1261
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1244
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
5 months
3
16
1178
0
2
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
2 years
1141
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
23 months
1
1
1122
0
0
Build graph with jRuby (...)
Matteo Picciolini
20 months
...
1045
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
20 months
1
...
1024
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
8 months
1
...
955
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
6 months
3
...
880
0
0
Generalized linear models for statsample (...)
Ankur Goel
7 months
...
830
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
15 months
...
795
Parser to work with file formats used in (...)
Ben J Woodcroft
3 weeks
...
698
2
9
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
10 months
2
...
574
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
6 weeks
...
562
0
10
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
3 months
...
538
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
9 months
...
510
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
3 months
...
507
0
3
Bio-repeatmasker (...)
Andrei Rozanski
3 months
504
Vcf parser (...)
Pjotr Prins
7 weeks
1
413
0
83
A parser for cigar format alignments (...)
Ben J Woodcroft
7 weeks
2
...
346
(...) pre
pre
333
!
Biostars data-mining and statistical analysis (...) new
Joachim Baran
2 weeks
...
314
0
16
Mine publications for gene names (...)
Pjotr Prins
7 weeks
...
172
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
6 weeks
2
...
142
0
3
!
Tool to work with polyploids, ngs and molecular (...) new
Ricardo H.  Ramirez-Gonzalez
3 weeks
...
120
0
25
!
Bindings to some internals of the velvet assembler (...) new
Ben Woodcroft
3 weeks
...
120
7
21
!
(...) new
pre
54
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-04-23
**) number of commits on GitHub (last 7 days & last 90 days)