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
24 months
266
11
91833
5927
Parser of scientific names (...) !
Dmitry Mozzherin
1 week
19
5
50019
4691
0
15
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
6 days
6
2
42078
2604
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
12 months
14
11
38544
2316
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
2 months
19
6
38448
4974
0
9
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
2 months
2
...
29847
2002
0
6
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
14 months
13
1
25278
1752
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
23 months
1
25201
2572
0
0
Http requests to entrez e-utilities (...)
Jared Ning
4 weeks
4
...
24261
1499
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
6 days
23897
4379
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
5
23207
1048
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
14 months
22723
1240
Create pretty svg-format images of features, gene models (...)
Dan MacLean
16 months
10
5
20958
3493
0
0
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
18894
1035
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
18207
1286
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
16039
902
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
15827
1202
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
2 weeks
12
1
15114
1610
0
5
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
15055
828
0
0
A simple obo file handler (...) !
mjy
3 years
4
...
14034
767
0
0
A fast parser for fastq files (...)
Francesco Strozzi
2 years
10
...
11343
767
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
12 months
8
5
11138
742
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
11 months
9
20
11108
930
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
4 months
12
2
11075
1491
0
3
Data mining algorithms for jRuby (...)
arrigonialberto86
20 months
14
3
9871
1115
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
1
...
9551
607
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9424
508
0
0
Low memory sequence emitters (...)
Pjotr Prins
12 months
8
1
9132
623
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
8929
440
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
9 months
3
...
8586
634
0
0
Ruby support for the baclava file format (...) !
Robert Haines
14 months
1
...
8464
555
Build genome output files (...)
Michael Barton
21 months
5
...
8461
413
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8210
412
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
2
2
8191
2489
0
11
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
8026
374
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7990
505
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
24 months
5
...
7771
597
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
23 months
8
...
7760
409
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
7724
422
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7649
499
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
14 months
...
7573
484
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7540
428
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7485
299
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6973
318
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
6867
328
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
30
14
6642
398
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6251
310
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5985
443
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
21 months
12
2
5737
707
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5581
320
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5443
237
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
5361
307
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
2
1
5191
414
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5168
314
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
2 months
4
3
5076
886
0
6
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
4943
194
0
0
Ruby binding for samtools tabix (...)
throwern
20 months
3
...
4910
394
Parser to work with file formats used in (...)
Ben J Woodcroft
4 months
...
4436
863
Fast multi-threaded vcf parser (...)
Pjotr Prins
4 months
18
7
4372
919
0
4
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4338
300
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4288
304
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4265
314
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4253
301
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4193
211
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4160
216
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
3942
229
0
0
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3903
227
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
11 weeks
...
3678
1192
0
5
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
20 months
3674
375
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3627
203
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3465
287
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3464
208
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3411
206
0
0
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3370
314
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
21 months
1
...
3358
312
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
3078
205
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3010
204
0
0
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
2 weeks
2995
2645
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2916
204
Publish scientific results to the semantic web (...) !
Will Strinz
11 months
3
16
2743
323
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
14 months
1
...
2546
408
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
4 months
1
2301
598
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2166
106
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2161
107
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2154
103
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2139
523
0
25
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2065
84
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
6 months
1
2034
692
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
15 months
6
...
2033
127
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
21 months
1
...
1935
208
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
1905
112
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1878
95
0
0
Biostars data-mining and statistical analysis (...)
Joachim Baran
13 months
1875
314
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1869
109
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1855
99
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1849
423
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
20 months
3
...
1847
202
0
2
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1838
103
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1828
103
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1815
106
Generalized linear models for statsample (...)
Ankur Goel
20 months
1800
206
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1787
98
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1781
107
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1749
102
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1742
101
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 years
1
1
1659
107
Build graph with jRuby (...)
Matteo Picciolini
2 years
1557
104
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
16 months
...
1557
219
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
3
...
1551
112
Interface for express beta diversity (...)
Ben J. Woodcroft
16 months
...
1533
212
Bio-repeatmasker (...)
Andrei Rozanski
16 months
1499
203
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1456
313
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
15 months
4
...
1388
224
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1302
107
0
0
Web server for bio-samtools (...)
homonecloco
11 months
...
1246
229
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
23 months
2
...
1094
112
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
7 months
1033
220
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
22 months
...
1026
106
0
0
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
89
1
736
153
0
0
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
5 months
1
...
726
251
0
0
Mine publications for gene names (...)
Pjotr Prins
14 months
...
696
105
0
0
Helper methods for reading .delta files (...)
robsyme
7 weeks
...
638
513
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
14 months
614
82
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
10 months
1
...
548
111
0
0
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
8 months
...
509
126
0
0
Tools to work with fasta files, indexed with (...)
homonecloco
7 months
...
467
116
0
0
Tools to manipulate blat files from the command (...)
homonecloco
7 months
...
450
107
(...) pre
pre
419
26
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
6 months
...
409
117
0
0
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
6 months
...
407
123
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
381
81
!
Api of picard tool (...) new
Natapol Pornputtapong
3 days
239
118
!
The api for freebayes version #{bio::freebayes::extversion} (...) new
Natapol Pornputtapong
2 days
236
204
Bioinformatics. aggregate fastqc (quality control for next generation (...)
Raoul Jean Pierre Bonnal
9 weeks
...
214
214
A pipeline manager (...)
Francesco Strozzi
8 weeks
8
10
203
203
A web app wrapper for genevalidator (...) !
Ismail Moghul
2 days
...
187
187
(...) pre
pre
174
37
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
2 days
114
114
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-05-24
**) number of commits on GitHub (last 7 days & last 90 days)