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
21 months
263
12
86553
7232
Parser of scientific names (...) !
Dmitry Mozzherin
6 months
18
5
45700
4485
0
0
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
6 weeks
5
1
39697
2983
0
3
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
9 months
14
11
36472
3224
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
6 days
17
6
34220
5537
6
12
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
6 days
2
...
28140
2009
6
10
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
11 months
13
1
23719
2418
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
22884
2090
Gadgets for bioinformatics (...)
Shintaro Katayama
21 months
...
22861
3121
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
4
22265
1429
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
11 months
21610
1466
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
2 months
55
29
19704
2156
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
17966
1409
Create pretty svg-format images of features, gene models (...)
Dan MacLean
14 months
9
5
17898
3978
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
17039
1953
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
1
...
15232
1128
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
14749
1690
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
14301
1392
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
3 months
12
...
13624
2062
2
2
A simple obo file handler (...) !
mjy
3 years
4
...
13347
905
0
0
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
10654
995
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
9 months
7
5
10469
1090
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
9 months
8
20
10276
1271
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
8 weeks
11
2
9754
2313
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
1
...
9008
868
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
8966
697
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
17 months
14
3
8866
1552
Low memory sequence emitters (...)
Pjotr Prins
9 months
8
1
8578
852
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
8539
490
0
0
Build genome output files (...)
Michael Barton
18 months
5
...
8093
516
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
7 months
1
...
8023
875
0
0
Ruby support for the baclava file format (...) !
Robert Haines
12 months
1
...
7965
461
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
7839
559
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7688
462
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7537
710
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
20 months
8
...
7391
680
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
7348
583
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
21 months
5
...
7239
837
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7217
661
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7199
709
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7160
585
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
11 months
...
7136
569
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6693
441
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6578
518
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
6279
442
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5975
422
0
0
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
2 weeks
2
1
5919
2348
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5580
660
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
5292
431
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
5233
404
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
19 months
11
2
5109
963
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
5088
436
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4887
439
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
22 months
2
1
4824
570
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
38
5
4768
227
Ruby binding for samtools tabix (...)
throwern
17 months
3
...
4561
567
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
5 days
4
3
4373
948
6
9
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4070
432
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4015
441
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4003
282
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
3987
428
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3983
415
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
3969
287
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3733
306
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3702
316
Parser to work with file formats used in (...)
Ben J Woodcroft
7 weeks
...
3676
1324
0
8
Fast multi-threaded vcf parser (...)
Pjotr Prins
9 weeks
15
7
3558
1329
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3446
279
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
17 months
3342
582
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3276
291
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3231
290
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3207
421
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
21 months
...
3091
434
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
18 months
1
...
3079
427
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2897
295
0
0
A protparam compatible utility for BioRuby (...)
hryk
2 years
1
...
2829
287
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2735
289
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
4 months
...
2576
1049
Publish scientific results to the semantic web (...) !
Will Strinz
8 months
3
16
2451
348
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
11 months
1
...
2184
566
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2072
130
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2067
152
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2063
152
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
1990
146
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
13 months
6
...
1918
164
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1805
140
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1794
138
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
7 weeks
1
1775
971
0
9
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1771
145
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1770
153
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1750
149
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
18 months
1
...
1749
283
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1736
142
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1720
141
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1699
147
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1686
152
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
17 months
3
1
1668
285
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1657
136
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1654
146
A general purpose framework for scripted handling of (...) development/stable
mjy
23 months
2
...
1628
159
Generalized linear models for statsample (...)
Ankur Goel
17 months
1613
283
Biostars data-mining and statistical analysis (...)
Joachim Baran
11 months
1599
440
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1564
156
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
1465
152
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1450
144
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1435
98
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
3 months
...
1431
721
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
13 months
...
1361
286
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
13 months
...
1347
297
0
0
Bio-repeatmasker (...)
Andrei Rozanski
13 months
1322
282
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1205
147
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
5
...
1188
352
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
12 months
4
...
1185
291
0
0
Web server for bio-samtools (...)
homonecloco
9 months
...
1043
297
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
20 months
2
...
996
155
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
19 months
...
933
149
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
4 months
841
311
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
90
1
607
188
Mine publications for gene names (...)
Pjotr Prins
12 months
...
603
149
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
11 months
542
183
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
11 weeks
1
...
511
511
0
11
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
7 months
1
...
451
160
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
5 months
...
397
182
0
0
(...) pre
pre
395
22
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
6 weeks
386
386
Tools to work with fasta files, indexed with (...)
homonecloco
4 months
...
365
167
Tools to manipulate blat files from the command (...)
homonecloco
5 months
...
359
159
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
310
91
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
3 months
...
306
168
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
3 months
...
299
162
0
0
!
Helper methods for reading .delta files (...) new
robsyme
3 weeks
...
147
147
0
11
(...) pre
pre
140
28
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-03-04
**) number of commits on GitHub (last 7 days & last 90 days)