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
18 months
30
12
78768
9859
0
18
Parser of scientific names (...) !
Dmitry Mozzherin
3 months
16
5
40712
2865
0
0
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
8 months
5
1
36434
5181
0
0
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
6 months
14
11
32862
1984
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
6 weeks
17
5
28225
2619
0
0
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
9 weeks
2
...
25897
4702
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
8 months
13
1
21003
1515
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
20627
1156
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
8 months
...
19938
4452
Gadgets for bioinformatics (...)
Shintaro Katayama
17 months
...
19384
1887
0
0
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
10 months
30
22
17406
1198
0
93
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
16393
872
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
14960
1114
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
14009
775
Create pretty svg-format images of features, gene models (...)
Dan MacLean
10 months
9
5
13606
1638
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
12854
1041
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
12728
1387
0
0
A simple obo file handler (...) !
mjy
3 years
4
...
12346
561
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
3 weeks
11
...
11290
2029
0
66
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
9551
647
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
6 months
7
5
9256
632
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
6 months
7
20
8849
827
0
0
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
8182
445
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
21 months
1
...
8037
528
0
7
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
7996
327
Low memory sequence emitters (...)
Pjotr Prins
6 months
8
1
7625
530
0
0
Build genome output files (...)
Michael Barton
15 months
3
...
7533
366
Ruby support for the baclava file format (...) !
Robert Haines
8 months
1
...
7388
3733
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 days
9
2
7234
1036
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
7210
352
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7179
323
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
14 months
14
3
7134
956
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
3 months
1
...
7044
554
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
24 months
2
...
6742
450
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
6699
347
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
17 months
8
...
6659
366
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6511
249
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6503
366
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
8 months
...
6449
4242
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6404
438
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
18 months
5
...
6301
538
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
6198
273
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6009
312
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5776
302
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5506
268
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
4853
380
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4809
282
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
4800
196
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4599
269
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
5
4520
166
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4400
249
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
19 months
2
1
4187
351
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
15 months
11
2
4047
832
0
0
Ruby binding for samtools tabix (...)
throwern
14 months
3
...
3926
369
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3686
179
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3649
172
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3591
271
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3523
265
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3516
262
0
0
Next-generation mapping of mutations (...)
Dan MacLean
24 months
2
...
3506
269
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3389
198
0
9
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3346
201
Taverna player is a rails plugin to run (...)
Robert Haines
4 weeks
4
3
3344
768
0
36
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
4 weeks
2
...
3263
2128
0
33
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3132
175
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2951
173
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2904
178
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
21 months
...
2737
262
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
14 months
...
2696
354
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
18 months
...
2608
246
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
15 months
1
...
2597
272
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2566
174
0
0
A protparam compatible utility for BioRuby (...)
hryk
23 months
1
...
2511
180
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2415
180
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
4 months
...
2251
558
0
0
Fast multi-threaded vcf parser (...)
Pjotr Prins
2 days
13
8
2086
909
9
59
Publish scientific results to the semantic web (...) !
Will Strinz
5 months
3
16
2066
267
0
5
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1924
96
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1898
87
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1895
89
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1831
75
0
0
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
9 months
6
...
1738
114
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1645
92
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1640
88
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1610
92
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1597
97
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1586
90
0
0
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1572
90
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1561
105
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
8 months
1
...
1547
370
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1536
95
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1516
85
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1504
93
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1492
95
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
20 months
1
...
1456
98
Gggenome Ruby client (...)
Mitsuteru Nakao
15 months
1
...
1433
172
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
6 weeks
...
1387
955
0
8
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1387
100
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
14 months
3
1
1351
176
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1327
68
Generalized linear models for statsample (...)
Ankur Goel
14 months
...
1300
172
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1294
94
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1289
91
0
0
Biostars data-mining and statistical analysis (...)
Joachim Baran
7 months
...
1109
283
0
0
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
22 months
...
1042
92
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
10 months
...
1035
190
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
10 months
...
1015
198
0
0
Bio-repeatmasker (...)
Andrei Rozanski
10 months
1003
189
A parser for cigar format alignments (...)
Ben J Woodcroft
9 months
4
...
857
198
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
17 months
2
...
826
92
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
804
328
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
16 months
...
769
101
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
6 months
1
763
189
0
0
Web server for bio-samtools (...)
homonecloco
6 months
...
711
194
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
3 weeks
...
666
666
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
7 weeks
...
496
268
Mine publications for gene names (...)
Pjotr Prins
9 months
...
433
98
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
5 years
30
1
398
171
0
0
(...) pre
pre
370
14
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
8 months
2
...
350
75
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
4 months
...
274
112
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
5 years
209
93
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
9 weeks
...
195
130
0
22
Tools to manipulate blat files from the command (...)
homonecloco
8 weeks
...
181
181
Tools to work with fasta files, indexed with (...)
homonecloco
7 weeks
...
176
176
!
Faldo location output method for bio::location in BioRuby (...) new
Joachim Baran, Naohisa Goto
2 weeks
...
117
117
0
16
!
Emulates as if old BioRuby biofetch alives (...) new
Naohisa Goto
2 weeks
...
116
116
(...) pre
pre
107
19
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-11-28
**) number of commits on GitHub (last 7 days & last 90 days)