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
15 months
30
17
68144
2869
0
2
Parser of scientific names (...) !
Dmitry Mozzherin
1 week
14
5
37489
1165
0
7
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
4 months
4
1
30817
1393
0
0
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 months
14
11
30629
716
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
11 weeks
17
5
25377
921
0
56
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
3 months
2
...
20837
1107
0
50
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
4 months
13
1
19297
540
0
0
Http requests to entrez e-utilities (...)
Jared Ning
3 years
4
...
19295
373
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
14 months
...
17250
686
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
6 months
30
30
15978
422
0
43
Gff3 parser for big data (...) !
Pjotr Prins
24 months
6
2
15397
314
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
5 months
...
15174
1061
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
30
13700
403
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
13073
291
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
7 months
7
5
11812
666
A biogem to submit jobs on a queue (...)
Francesco Strozzi
22 months
5
...
11679
374
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
11257
211
0
0
Very fast blast xml parser and library for (...) !
Pjotr Prins
18 months
9
...
9176
229
0
0
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
8825
229
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
3 months
6
4
8543
253
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
11 weeks
7
20
7927
297
0
14
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
7679
163
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
18 months
1
...
7440
176
Build genome output files (...)
Michael Barton
12 months
3
...
7089
139
0
0
Low memory sequence emitters (...)
Pjotr Prins
3 months
8
1
7026
206
0
6
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
6806
122
0
0
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
2 weeks
1
...
6416
245
0
3
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
1
6302
127
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
20 months
2
...
6232
162
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
13 months
6
...
6231
117
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
6211
85
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
12 months
8
3
6110
247
0
12
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6090
134
0
0
Data mining algorithms for jRuby (...)
arrigonialberto86
11 months
14
3
6062
336
0
0
Ruby wrapper for sambamba tool (...)
Artem Tarasov
24 months
2
...
5908
156
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
5889
103
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
14 months
5
...
5695
188
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5660
112
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5431
100
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5205
98
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
3 years
8
...
4563
68
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4487
104
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
4422
136
0
0
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
4
4314
55
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4296
102
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
21 months
2
...
4114
96
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
16 months
2
1
3792
128
0
0
Ruby support for the baclava file format (...) !
Robert Haines
5 months
1
...
3519
833
Ruby binding for samtools tabix (...)
throwern
10 months
3
...
3501
148
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3479
68
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3452
67
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
3286
98
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3221
100
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
22 months
2
...
3217
111
0
0
Next-generation mapping of mutations (...)
Dan MacLean
20 months
2
...
3201
104
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3164
73
4
84
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3115
70
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
12 months
11
2
3109
185
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
2 years
1
...
2930
65
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2747
64
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2698
65
0
0
Taverna player is a rails plugin to run (...)
Robert Haines
8 weeks
4
...
2461
204
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
18 months
...
2443
98
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2366
67
0
0
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
15 months
...
2326
100
A protparam compatible utility for BioRuby (...)
hryk
20 months
1
...
2306
68
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
11 months
...
2297
139
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
12 months
1
...
2288
102
0
0
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
21 months
2
...
2211
69
0
0
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
5 months
...
2069
834
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1812
35
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1795
32
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
2 years
1
1792
32
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
10 weeks
3
16
1746
133
0
3
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1739
23
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
5 weeks
...
1623
326
0
10
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1538
36
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
2 years
1
...
1537
37
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
2 years
...
1502
42
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
2 years
2
...
1486
37
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1481
37
One-line summary of your gem (...)
Toshiaki Katayama
2 years
1
...
1470
39
0
0
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
2 years
3
...
1439
37
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1426
36
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1415
34
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1395
35
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1382
37
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1271
36
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
...
1245
24
Gggenome Ruby client (...)
Mitsuteru Nakao
12 months
1
...
1236
63
0
0
Build graph with jRuby (...)
Matteo Picciolini
2 years
...
1183
37
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
1
...
1182
37
0
0
Ruby ensembl rest api (...)
Alberto Donizetti
10 months
3
1
1149
69
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
5 months
...
1127
138
0
0
Vcf parser (...)
Pjotr Prins
8 weeks
12
6
1123
174
Generalized linear models for statsample (...)
Ankur Goel
11 months
...
1100
69
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
11 weeks
...
1085
169
0
12
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
19 months
...
934
36
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
7 months
...
821
69
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
7 months
...
793
74
0
0
Bio-repeatmasker (...)
Andrei Rozanski
7 months
788
76
Biostars data-mining and statistical analysis (...)
Joachim Baran
4 months
...
781
120
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
14 months
2
...
720
39
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
13 months
...
653
37
A parser for cigar format alignments (...)
Ben J Woodcroft
5 months
3
...
636
70
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
2 months
1
548
87
0
7
Web server for bio-samtools (...)
homonecloco
11 weeks
...
488
93
!
Server for polymarker. to be used with cron (...) new
Ricardo H.  Ramirez-Gonzalez
4 weeks
...
385
385
0
9
(...) pre
pre
353
4
Mine publications for gene names (...)
Pjotr Prins
5 months
...
319
39
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
5 months
2
...
261
30
0
0
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
10 weeks
...
214
52
!
Ruby inferface for kseq.h by heng li for (...) new
Fedor Gusev
5 weeks
...
146
143
0
21
(...) pre
pre
83
5
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-08-20
**) number of commits on GitHub (last 7 days & last 90 days)