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
19 months
30
12
80383
9375
Parser of scientific names (...) !
Dmitry Mozzherin
4 months
18
5
41617
3078
0
0
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
8 months
5
1
37124
4932
0
0
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
7 months
14
11
33528
2141
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
8 weeks
17
5
29243
3043
0
0
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
12 weeks
2
...
26443
4387
0
10
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
8 months
13
1
21515
1642
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
20960
1282
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
9 months
...
20391
4056
Gadgets for bioinformatics (...)
Shintaro Katayama
18 months
...
20003
2022
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
1 week
30
18
17860
1447
12
122
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
16678
940
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
15333
1203
Create pretty svg-format images of features, gene models (...)
Dan MacLean
11 months
9
5
14362
2054
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
14260
906
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
13200
1119
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
13109
1494
A simple obo file handler (...) !
mjy
3 years
4
...
12538
685
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
5 weeks
11
...
11815
2010
0
9
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
9741
664
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
7 months
7
5
9469
692
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
6 months
7
20
9118
898
0
0
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
1
1
8328
475
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
22 months
1
...
8214
559
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
8099
393
0
0
Low memory sequence emitters (...)
Pjotr Prins
7 months
8
1
7799
569
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
today
10
2
7674
1300
1
40
Build genome output files (...)
Michael Barton
16 months
5
...
7651
427
0
0
Ruby support for the baclava file format (...) !
Robert Haines
9 months
1
...
7601
3186
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
15 months
14
3
7447
1028
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
7332
383
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7282
373
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
4 months
1
...
7220
585
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
6883
475
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
6813
373
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
17 months
8
...
6763
403
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
9 months
...
6661
3674
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6626
398
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6592
299
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6549
470
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
18 months
5
...
6475
575
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
6290
289
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
6103
329
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5869
332
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5590
282
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
4973
411
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4898
301
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
4861
230
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4688
288
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
30
5
4571
191
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4489
273
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
20 months
2
1
4302
373
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
16 months
11
2
4219
775
0
0
Ruby binding for samtools tabix (...)
throwern
14 months
3
...
4043
391
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
7 weeks
2
...
3756
2527
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3740
189
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3704
187
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3679
292
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3610
288
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3605
288
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
3593
288
Taverna player is a rails plugin to run (...)
Robert Haines
6 weeks
4
3
3540
910
0
36
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3453
214
0
6
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3411
218
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3194
196
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3010
187
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2965
199
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
22 months
...
2821
281
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
15 months
...
2808
385
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
19 months
...
2692
269
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
16 months
1
...
2688
295
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2627
190
A protparam compatible utility for BioRuby (...)
hryk
24 months
1
...
2571
195
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2473
192
Parser to work with file formats used in (...)
Ben J Woodcroft
5 months
...
2425
595
Fast multi-threaded vcf parser (...)
Pjotr Prins
3 weeks
13
8
2317
903
0
33
Publish scientific results to the semantic web (...) !
Will Strinz
6 months
3
16
2146
307
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1956
102
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1926
93
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1924
96
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1854
82
0
0
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
10 months
6
...
1773
134
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1676
99
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1668
94
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
9 months
1
...
1662
394
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1637
97
0
0
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1632
106
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1615
95
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
9 weeks
...
1610
1090
0
8
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1603
101
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1590
113
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1565
99
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1545
94
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1533
100
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1519
98
A general purpose framework for scripted handling of (...) development/stable
mjy
21 months
1
...
1493
122
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
16 months
1
...
1492
186
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1419
106
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
14 months
3
1
1408
192
Generalized linear models for statsample (...)
Ankur Goel
15 months
...
1352
183
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1348
77
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1326
102
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1319
98
0
0
Biostars data-mining and statistical analysis (...)
Joachim Baran
8 months
...
1193
301
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
11 months
...
1099
207
Interface for express beta diversity (...)
Ben J. Woodcroft
11 months
...
1079
214
0
0
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
23 months
...
1069
97
Bio-repeatmasker (...)
Andrei Rozanski
11 months
1063
199
A parser for cigar format alignments (...)
Ben J Woodcroft
9 months
4
...
918
211
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
870
327
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
18 months
2
...
854
98
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
6 months
1
829
212
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
17 months
...
795
104
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
5 weeks
...
781
781
0
7
Web server for bio-samtools (...)
homonecloco
6 months
...
770
207
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
9 weeks
...
557
307
Mine publications for gene names (...)
Pjotr Prins
9 months
...
465
106
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
5 years
30
1
436
170
0
0
(...) pre
pre
374
16
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
9 months
2
...
370
84
0
0
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
5 months
...
304
113
0
0
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
12 weeks
...
231
166
0
18
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
5 years
226
88
Tools to manipulate blat files from the command (...)
homonecloco
10 weeks
...
212
212
Tools to work with fasta files, indexed with (...)
homonecloco
10 weeks
...
211
211
!
A sequence read archive (sra) download script and (...) new
Ben J. Woodcroft
2 days
1
...
166
166
!
Faldo location output method for bio::location in BioRuby (...) new
Joachim Baran, Naohisa Goto
5 weeks
...
152
152
!
Emulates as if old BioRuby biofetch alives (...) new
Naohisa Goto
4 weeks
...
150
150
(...) pre
pre
113
23
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-12-17
**) number of commits on GitHub (last 7 days & last 90 days)