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
8 weeks
272
11
98024
5741
0
39
Parser of scientific names (...) !
Dmitry Mozzherin
2 days
19
3
55090
4641
7
24
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
3 months
6
2
45026
2683
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
10 weeks
22
6
41867
3116
0
4
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
15 months
15
12
41133
2341
0
0
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
6 months
2
...
31832
1806
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
2 years
1
27652
2218
0
0
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
17 months
14
1
27187
1727
0
0
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
3 months
26525
2383
Http requests to entrez e-utilities (...)
Jared Ning
4 months
5
...
25809
1410
A Ruby api for interacting with biomart services (...) !
Darren Oakley
4 years
18
5
24398
1073
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
17 months
24300
1451
Create pretty svg-format images of features, gene models (...)
Dan MacLean
20 months
10
5
22803
1679
0
0
Gff3 parser for big data (...) !
Pjotr Prins
3 years
6
2
20043
1032
0
0
Maf parser for BioRuby (...)
Clayton Wheeler
3 years
10
31
19678
1336
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
17186
1231
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
17152
1001
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
3 months
12
1
16774
1477
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
16075
886
0
0
A simple obo file handler (...) !
mjy
4 years
5
...
14934
830
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
7 months
12
3
12703
1476
0
1
A fast parser for fastq files (...)
Francesco Strozzi
3 years
10
...
12164
742
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
15 months
9
20
12155
944
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
15 months
8
5
11987
773
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
23 months
14
3
11110
1119
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
2
1
11014
2410
0
6
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
10242
622
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9987
509
0
0
Low memory sequence emitters (...)
Pjotr Prins
15 months
8
1
9815
612
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
9434
462
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
13 months
3
...
9257
603
0
0
Ruby support for the baclava file format (...) !
Robert Haines
18 months
1
...
9045
556
0
0
Build genome output files (...)
Michael Barton
2 years
5
...
8992
484
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8662
405
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
8568
522
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
4 years
1
...
8506
432
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
2 years
5
...
8458
621
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
3 years
2
...
8231
517
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
2 years
8
...
8216
418
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
3 years
7
2
8172
402
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
17 months
...
8028
423
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
8014
427
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
6 years
7834
318
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
7325
315
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
7230
329
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
14
7200
522
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
4 years
1
...
6601
319
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
3 years
2
...
6481
453
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
2 years
13
2
6422
616
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
6 months
4
3
5978
819
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5942
327
0
0
A plugin that allows you to parse large (...)
robsyme
4 years
1
...
5715
321
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5715
252
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
5644
413
Fast multi-threaded vcf parser (...)
Pjotr Prins
1 week
21
3
5536
1068
0
47
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5510
312
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
7 months
...
5358
838
Ruby binding for samtools tabix (...)
throwern
23 months
3
...
5355
399
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
39
5
5204
236
0
0
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
5 months
...
4745
966
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
3 years
4692
320
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
3 years
1
1
4649
323
0
0
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4613
315
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4589
307
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4442
225
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4405
221
0
0
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
2 months
4273
1203
Bioinformatics triple-store support (...)
Pjotr Prins
3 years
4
1
4212
248
0
0
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
4195
268
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
23 months
4127
402
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
4 years
1
...
3865
219
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3804
304
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
2 years
...
3723
315
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
3 years
2
...
3703
216
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
2 years
1
...
3702
316
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3657
224
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
14 months
3
16
3485
709
Parse pfam hmm definition files (...)
Ben J. Woodcroft
3 years
1
...
3329
224
0
0
A protparam compatible utility for BioRuby (...)
hryk
2 years
2
...
3242
209
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
3164
223
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
17 months
1
...
2989
404
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
2961
779
0
3
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
7 months
1
2925
567
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
9 months
1
2407
340
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2292
118
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2286
108
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2283
116
0
0
Biostars data-mining and statistical analysis (...)
Joachim Baran
16 months
2238
330
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
18 months
6
...
2217
168
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2185
111
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
2 years
1
...
2166
211
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
23 months
3
...
2091
221
0
0
Specimens quickly extracted and digitized, or just "squid" (...) alpha
Matt Yoder, Rich Flood
11 weeks
...
2078
2078
0
25
Generalized linear models for statsample (...)
Ankur Goel
23 months
2043
220
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
2038
122
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
4 years
1
...
1993
105
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1989
111
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1987
119
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
3 weeks
2
1
1975
303
0
3
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1966
115
0
0
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1949
112
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
4 years
1
...
1943
89
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1941
115
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
3 years
3
...
1922
121
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1907
114
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1875
114
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1867
112
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
19 months
...
1794
213
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
6 years
5
...
1794
316
Interface for express beta diversity (...)
Ben J. Woodcroft
19 months
...
1778
223
0
0
Bio-repeatmasker (...)
Andrei Rozanski
19 months
1733
211
Build graph with jRuby (...)
Matteo Picciolini
3 years
1690
123
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
3 years
3
...
1677
115
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
18 months
4
...
1633
220
0
0
Web server for bio-samtools (...)
homonecloco
15 months
...
1492
224
Identifying problems with gene predictions (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
3 weeks
...
1466
1146
0
94
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1422
108
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
10 months
1274
219
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
89
1
1223
475
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
2 years
2
...
1223
116
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
2 years
...
1152
113
0
0
Helper methods for reading .delta files (...)
robsyme
5 months
...
1044
377
0
0
Retrieve dna sequence from ucsc using given coordinates (...)
Andrei Rozanski
2 weeks
990
990
A web app wrapper for genevalidator (...) !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
3 weeks
...
979
745
0
0
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
8 months
1
...
975
229
0
0
Mine publications for gene names (...)
Pjotr Prins
18 months
...
820
113
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
17 months
723
100
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
13 months
1
...
682
118
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
11 months
...
647
125
0
0
Tools to work with fasta files, indexed with (...)
homonecloco
10 months
...
600
119
0
0
Tools to manipulate blat files from the command (...)
homonecloco
11 months
...
583
118
Aggregate fastqc (quality control for next generation sequencing (...)
Raoul Jean Pierre Bonnal
9 weeks
...
569
339
0
10
The api for freebayes version #{bio::freebayes::extversion} (...)
Natapol Pornputtapong
3 months
566
279
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
9 months
...
546
123
0
0
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
9 months
...
537
116
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
476
89
(...) pre
pre
458
38
Api of picard tool (...)
Natapol Pornputtapong
3 months
408
145
A pipeline manager (...)
Francesco Strozzi
5 months
11
11
364
151
0
0
(...) pre
pre
215
40
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-08-29
**) number of commits on GitHub (last 7 days & last 90 days)