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
77766
9414
5
18
Parser of scientific names (...) !
Dmitry Mozzherin
3 months
16
5
40457
2905
0
0
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
7 months
5
1
35875
4802
0
0
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
6 months
14
11
32689
2022
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
5 weeks
17
5
27833
2422
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
8 weeks
2
...
25448
4427
0
5
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
7 months
13
1
20873
1548
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
20548
1179
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
8 months
...
19528
4197
Gadgets for bioinformatics (...)
Shintaro Katayama
17 months
...
19219
1932
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
9 months
30
22
17240
1133
1
93
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
16318
900
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
14862
1134
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
13892
730
Create pretty svg-format images of features, gene models (...)
Dan MacLean
10 months
9
5
13283
1448
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
12764
1062
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
12577
1296
0
0
A simple obo file handler (...) !
mjy
3 years
4
...
12298
585
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
1 week
11
...
11102
1910
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
9497
658
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
6 months
7
5
9206
646
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
5 months
7
20
8782
839
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
8143
455
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
21 months
1
...
7994
542
A nexus file format (phylogenetic inference) parser in (...) !
mjy
3 years
1
...
7968
347
0
0
Low memory sequence emitters (...)
Pjotr Prins
6 months
8
1
7578
537
Build genome output files (...)
Michael Barton
15 months
3
...
7474
345
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
7177
361
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7134
315
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
1 week
9
3
7061
936
Ruby support for the baclava file format (...) !
Robert Haines
8 months
1
...
7053
3479
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
14 months
14
3
7051
972
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
3 months
1
...
6999
568
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
23 months
2
...
6704
460
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
6665
353
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
17 months
8
...
6638
379
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6492
261
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6473
375
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
6364
446
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
17 months
5
...
6254
545
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
6172
277
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
8 months
...
6084
3969
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5984
317
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5759
302
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5485
274
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
4811
379
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4787
292
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
9
...
4784
202
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4573
271
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
5
4496
161
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
4378
257
Read and manipulate cd-hit clusters (...)
George Githinji
19 months
2
1
4156
356
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
15 months
11
2
3989
864
0
0
Ruby binding for samtools tabix (...)
throwern
13 months
3
...
3893
378
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3671
186
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3635
177
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3569
277
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3498
269
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
3490
263
0
0
Next-generation mapping of mutations (...)
Dan MacLean
23 months
2
...
3485
278
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3374
202
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3330
206
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
2 weeks
4
3
3281
755
0
36
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
3 weeks
2
...
3146
2054
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3117
181
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2937
183
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2889
185
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
21 months
...
2715
265
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
14 months
...
2663
357
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
18 months
...
2586
252
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
15 months
1
...
2577
283
0
0
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2552
181
0
0
A protparam compatible utility for BioRuby (...)
hryk
23 months
1
...
2492
180
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2399
183
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
4 months
...
2209
575
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
5 months
3
16
2043
269
Fast multi-threaded vcf parser (...)
Pjotr Prins
8 weeks
13
8
1943
811
0
53
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1915
98
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1892
93
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
1888
92
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1827
81
0
0
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
9 months
6
...
1723
114
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1639
96
0
0
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1633
92
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1602
94
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1590
100
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1579
95
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1565
92
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1553
109
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1530
100
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
8 months
1
...
1521
384
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1507
88
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1496
97
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1484
98
0
0
A general purpose framework for scripted handling of (...) development/stable
mjy
20 months
1
...
1443
95
Gggenome Ruby client (...)
Mitsuteru Nakao
15 months
1
...
1417
176
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1379
104
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
13 months
3
1
1338
183
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
5 weeks
...
1333
941
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1323
72
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1286
99
Generalized linear models for statsample (...)
Ankur Goel
14 months
...
1284
178
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1283
97
0
0
Biostars data-mining and statistical analysis (...)
Joachim Baran
7 months
...
1087
298
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
22 months
...
1035
97
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
10 months
...
1021
196
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
10 months
...
1001
204
0
0
Bio-repeatmasker (...)
Andrei Rozanski
10 months
989
196
A parser for cigar format alignments (...)
Ben J Woodcroft
8 months
4
...
842
201
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
17 months
2
...
819
95
0
0
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
4
...
786
358
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
16 months
...
759
102
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
6 months
1
749
195
0
0
Web server for bio-samtools (...)
homonecloco
5 months
...
697
202
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
2 weeks
...
607
607
0
7
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
5 weeks
...
477
260
Mine publications for gene names (...)
Pjotr Prins
8 months
...
423
100
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
5 years
30
1
392
185
0
0
(...) pre
pre
370
14
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
8 months
2
...
346
79
0
0
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
4 months
...
262
112
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
5 years
202
99
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
8 weeks
...
186
121
Tools to manipulate blat files from the command (...)
homonecloco
6 weeks
...
173
173
Tools to work with fasta files, indexed with (...)
homonecloco
6 weeks
...
166
166
0
4
(...) pre
pre
107
20
!
Faldo location output method for bio::location in BioRuby (...) new
Joachim Baran, Naohisa Goto
1 week
...
106
106
!
Emulates as if old BioRuby biofetch alives (...) new
Naohisa Goto
1 week
...
98
98
9
10
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-11-20
**) number of commits on GitHub (last 7 days & last 90 days)