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
20 months
30
12
83634
8530
Parser of scientific names (...) !
Dmitry Mozzherin
5 months
18
5
43478
3784
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
2 weeks
5
1
38596
4466
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
8 months
14
11
34882
2742
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
3 months
17
5
31439
4298
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
4 months
2
...
27255
3346
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
10 months
13
1
22521
2077
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
21755
1616
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
4
21563
1232
Gadgets for bioinformatics (...)
Shintaro Katayama
19 months
...
21322
2621
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
10 months
...
21027
3016
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
7 weeks
30
17
18687
1824
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
17279
1208
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
16089
1588
Create pretty svg-format images of features, gene models (...)
Dan MacLean
12 months
9
5
16054
3198
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
14753
1122
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
13908
1432
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
13845
1699
A simple obo file handler (...) !
mjy
3 years
4
...
12932
862
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
11 weeks
12
...
12866
2397
0
9
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
10166
844
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
8 months
7
5
9901
882
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
8 months
8
20
9663
1112
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 weeks
10
2
8710
1987
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
1
1
8615
595
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
23 months
1
...
8592
736
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
8313
485
Low memory sequence emitters (...)
Pjotr Prins
8 months
8
1
8151
725
Data mining algorithms for jRuby (...)
arrigonialberto86
16 months
14
3
8114
1333
Build genome output files (...)
Michael Barton
17 months
5
...
7873
518
Ruby support for the baclava file format (...) !
Robert Haines
11 months
1
...
7818
1952
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
5 months
1
...
7572
725
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
7566
480
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7495
469
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7182
601
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
7055
486
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
19 months
8
...
7023
511
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
10 months
...
6919
2305
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6865
497
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6855
609
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
20 months
5
...
6830
726
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6812
421
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6469
373
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6293
394
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
6044
373
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5773
365
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5219
519
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
5087
379
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
4995
280
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4870
367
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
17 months
11
2
4681
882
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
3 months
2
...
4679
1989
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
30
5
4676
235
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4665
352
Read and manipulate cd-hit clusters (...)
George Githinji
21 months
2
1
4539
478
Ruby binding for samtools tabix (...)
throwern
16 months
3
...
4278
493
Taverna player is a rails plugin to run (...)
Robert Haines
3 months
4
3
3889
904
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
3863
244
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3858
369
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
3825
239
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3801
380
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
3777
368
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3769
351
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3590
273
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3539
265
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3308
244
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3141
252
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3078
244
Parser to work with file formats used in (...)
Ben J Woodcroft
2 weeks
...
3060
1004
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
16 months
...
3060
504
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
23 months
...
2995
354
Fast multi-threaded vcf parser (...)
Pjotr Prins
4 weeks
15
6
2938
1179
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
20 months
...
2874
355
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
17 months
1
...
2871
374
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2746
243
A protparam compatible utility for BioRuby (...)
hryk
2 years
1
...
2690
244
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2590
243
Publish scientific results to the semantic web (...) !
Will Strinz
7 months
3
16
2284
344
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
3 months
...
2044
929
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2012
123
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
1991
125
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1989
126
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1923
123
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
10 months
1
...
1904
494
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
11 months
6
...
1850
169
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1734
121
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1722
115
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1702
128
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1695
130
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1672
116
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1666
129
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1652
133
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1626
125
Gggenome Ruby client (...)
Mitsuteru Nakao
17 months
1
...
1614
243
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1605
122
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1592
123
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1577
120
A general purpose framework for scripted handling of (...) development/stable
mjy
22 months
1
...
1558
148
Ruby ensembl rest api (...)
Alberto Donizetti
16 months
3
1
1529
242
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1484
135
Generalized linear models for statsample (...)
Ankur Goel
16 months
...
1474
239
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1390
130
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1387
94
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1384
128
Biostars data-mining and statistical analysis (...)
Joachim Baran
9 months
1
...
1376
376
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
2 weeks
1
1375
683
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
12 months
...
1218
245
Interface for express beta diversity (...)
Ben J. Woodcroft
12 months
...
1199
255
Bio-repeatmasker (...)
Andrei Rozanski
12 months
1185
249
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1133
128
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
12 weeks
...
1061
683
A parser for cigar format alignments (...)
Ben J Woodcroft
11 months
4
...
1042
259
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
1018
351
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
19 months
2
...
918
123
Web server for bio-samtools (...)
homonecloco
8 months
...
895
257
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
18 months
...
857
128
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
3 months
...
683
273
Mine publications for gene names (...)
Pjotr Prins
11 months
...
528
135
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
30
1
514
180
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
10 months
2
...
429
113
(...) pre
pre
383
17
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
6 months
...
373
139
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
6 weeks
1
...
341
341
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
4 months
...
297
150
Tools to work with fasta files, indexed with (...)
homonecloco
3 months
...
287
154
Tools to manipulate blat files from the command (...)
homonecloco
3 months
...
276
138
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
270
97
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
11 weeks
...
227
227
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
11 weeks
...
225
225
(...) pre
pre
125
26
!
Rocker (...) new
Luis (Coto) Orellana, Luis M. Rodriguez-R
1 week
103
103
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-01-29
**) number of commits on GitHub (last 7 days & last 90 days)