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
4 weeks
269
11
96364
5691
Parser of scientific names (...) !
Dmitry Mozzherin
9 weeks
19
3
53172
4172
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
11 weeks
6
2
43853
2229
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
6 weeks
21
6
40668
3000
0
6
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
14 months
14
11
40160
2035
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
5 months
2
...
31186
1580
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
2 years
1
26721
1921
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
16 months
14
1
26468
1502
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
11 weeks
25363
1982
Http requests to entrez e-utilities (...)
Jared Ning
3 months
4
...
25236
1177
A Ruby api for interacting with biomart services (...) !
Darren Oakley
4 years
18
5
23954
944
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
16 months
23802
1250
Create pretty svg-format images of features, gene models (...)
Dan MacLean
19 months
10
5
22145
1771
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
19619
920
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
19112
1151
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
16674
1064
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
16672
766
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
2 months
12
1
16292
1593
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
15827
962
0
0
A simple obo file handler (...) !
mjy
3 years
5
...
14595
680
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
7 months
12
3
12091
1267
A fast parser for fastq files (...)
Francesco Strozzi
3 years
10
...
11860
660
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
14 months
9
20
11760
817
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
14 months
8
5
11657
653
Data mining algorithms for jRuby (...)
arrigonialberto86
22 months
14
3
10642
972
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
9 weeks
2
1
9998
2257
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
9980
543
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9783
453
0
0
Low memory sequence emitters (...)
Pjotr Prins
14 months
8
1
9555
539
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
9245
383
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
12 months
3
...
9003
526
0
0
Ruby support for the baclava file format (...) !
Robert Haines
17 months
1
...
8939
520
0
0
Build genome output files (...)
Michael Barton
24 months
5
...
8759
360
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8490
360
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
8356
459
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
4 years
1
...
8298
325
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
2 years
5
...
8198
537
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
2 years
8
...
8043
345
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
8013
459
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
7996
349
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
16 months
...
7913
406
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7842
382
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7703
271
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
7190
278
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
7091
282
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
14
6856
270
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6464
268
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
6295
392
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
24 months
13
2
6153
539
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5805
282
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
5 months
4
3
5630
659
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5610
209
0
0
A plugin that allows you to parse large (...)
robsyme
4 years
1
...
5578
273
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
5470
356
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5371
261
0
0
Ruby binding for samtools tabix (...)
throwern
22 months
3
...
5188
352
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
5077
165
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
7 months
20
6
5025
818
Parser to work with file formats used in (...)
Ben J Woodcroft
6 months
...
5016
725
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4549
266
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
3 years
1
1
4510
280
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4483
275
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4457
257
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
5 months
...
4361
853
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4337
185
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4311
193
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
4089
189
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
4065
200
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
22 months
3960
355
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
8 weeks
3844
1340
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3765
174
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3667
253
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3599
175
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3586
269
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
23 months
1
...
3571
267
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3551
178
Publish scientific results to the semantic web (...) !
Will Strinz
13 months
3
16
3243
539
Parse pfam hmm definition files (...)
Ben J. Woodcroft
3 years
1
...
3221
180
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3154
180
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
3065
190
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
17 months
1
...
2822
352
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
6 months
1
2694
496
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2608
591
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
9 months
1
2288
346
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2241
101
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2238
96
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2232
98
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2135
82
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
18 months
6
...
2130
116
Biostars data-mining and statistical analysis (...)
Joachim Baran
16 months
2102
279
Gggenome Ruby client (...)
Mitsuteru Nakao
24 months
1
...
2071
175
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
22 months
3
...
1994
184
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
1980
96
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1943
87
0
0
Generalized linear models for statsample (...)
Ankur Goel
22 months
1941
181
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1937
91
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1930
95
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1912
93
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
4 years
1
...
1903
66
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1896
90
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1890
97
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1869
103
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1854
92
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1824
95
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1817
96
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 years
1
1
1731
95
Specimens quickly extracted and digitized, or just "squid" (...) alpha
Matt Yoder, Rich Flood
7 weeks
...
1707
1707
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
18 months
...
1704
187
Interface for express beta diversity (...)
Ben J. Woodcroft
18 months
...
1683
189
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1666
248
Bio-repeatmasker (...)
Andrei Rozanski
18 months
1642
177
Build graph with jRuby (...)
Matteo Picciolini
2 years
1631
95
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
3
...
1627
94
A parser for cigar format alignments (...)
Ben J Woodcroft
17 months
4
...
1545
194
0
0
Web server for bio-samtools (...)
homonecloco
14 months
...
1395
191
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1373
92
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
9 months
1178
184
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
2 years
2
...
1169
99
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
90
1
1144
426
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
2 years
...
1102
100
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
6 days
...
997
997
0
118
Helper methods for reading .delta files (...)
robsyme
4 months
...
898
322
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
7 months
1
...
879
196
Mine publications for gene names (...)
Pjotr Prins
17 months
...
771
94
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
17 months
677
77
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
12 months
1
...
627
100
0
0
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
10 months
...
592
107
A web app wrapper for genevalidator (...) !
Ismail Moghul
2 days
...
556
556
Tools to work with fasta files, indexed with (...)
homonecloco
10 months
...
547
101
Tools to manipulate blat files from the command (...)
homonecloco
10 months
...
533
99
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
8 months
...
491
103
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
8 months
...
490
102
0
0
The api for freebayes version #{bio::freebayes::extversion} (...)
Natapol Pornputtapong
10 weeks
466
434
Aggregate fastqc (quality control for next generation sequencing (...)
Raoul Jean Pierre Bonnal
5 weeks
...
464
274
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
434
63
(...) pre
pre
427
12
Api of picard tool (...)
Natapol Pornputtapong
10 weeks
351
227
A pipeline manager (...)
Francesco Strozzi
4 months
11
10
303
127
0
0
(...) pre
pre
185
16
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-08-03
**) number of commits on GitHub (last 7 days & last 90 days)