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
14 months
30
17
66248
973
Parser of scientific names (...) !
Dmitry Mozzherin
7 months
14
5
36712
388
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
9 weeks
14
11
30156
243
0
3
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall
3 months
4
1
29961
537
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
8 weeks
17
4
24838
382
0
68
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
3 months
2
...
20157
427
0
147
Http requests to entrez e-utilities (...)
Jared Ning
2 years
4
...
19058
136
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
4 months
13
1
18947
190
0
0
Gadgets for bioinformatics (...)
Shintaro Katayama
13 months
...
16806
242
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Yannick Wurm
6 months
30
30
15720
164
4
52
Gff3 parser for big data (...) !
Pjotr Prins
23 months
6
2
15186
103
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
4 months
...
14534
421
Maf parser for BioRuby (...)
Clayton Wheeler
23 months
10
30
13447
140
0
0
Interfaces with biomodel search engine (...) !
Niall Beard
2 years
...
12896
114
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
21 months
5
...
11440
135
0
0
Create pretty svg-format images of features, gene models (...)
Dan MacLean
6 months
7
5
11439
293
0
0
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
2 years
4
2
11138
92
0
0
Very fast blast xml parser and library for (...) !
Pjotr Prins
17 months
9
...
9044
97
0
0
A fast parser for fastq files (...)
Francesco Strozzi
2 years
9
...
8680
84
0
0
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
10 weeks
6
4
8381
91
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
8 weeks
7
20
7734
104
0
14
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
2 years
1
1
7571
55
0
0
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
17 months
1
...
7324
60
0
0
Build genome output files (...)
Michael Barton
11 months
3
...
6999
49
0
0
Low memory sequence emitters (...)
Pjotr Prins
10 weeks
8
1
6896
76
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
3 years
4
...
6725
41
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
23 months
1
...
6224
53
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
1
6220
45
0
0
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
13 months
6
...
6153
39
0
0
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
4 years
6152
26
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
20 months
2
...
6126
56
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
2 years
3
...
6003
47
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
11 months
8
3
5954
91
1
11
Data mining algorithms for jRuby (...)
arrigonialberto86
10 months
13
3
5842
116
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
6 years
5820
34
Ruby wrapper for sambamba tool (...)
Artem Tarasov
23 months
2
...
5803
51
0
0
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
3 years
4
...
5591
43
0
0
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
14 months
5
...
5574
67
0
0
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
29
14
5372
41
0
0
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
5145
38
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
3 years
8
...
4515
20
0
0
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
3 years
4
...
4419
36
0
0
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
24 months
2
...
4336
50
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
3 years
30
4
4276
17
0
0
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
4228
34
0
0
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
20 months
2
...
4052
34
Read and manipulate cd-hit clusters (...)
George Githinji
15 months
2
1
3711
47
0
0
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
3 years
1
...
3433
22
0
0
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
2 years
1
...
3409
24
Ruby binding for samtools tabix (...)
throwern
10 months
3
...
3403
50
0
0
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
24 months
3224
36
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
3158
37
0
0
Ruby binding to the ucsc kent utilities (...)
throwern
22 months
2
...
3142
36
0
0
Next-generation mapping of mutations (...)
Dan MacLean
19 months
2
...
3133
36
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3120
29
32
75
Parse affymetrix cel/cdf files (...)
Pjotr Prins
2 years
2
1
3071
26
0
0
Ruby support for the baclava file format (...) !
Robert Haines
4 months
1
...
3029
343
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
11 months
9
2
2991
67
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
2 years
1
...
2892
27
0
0
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
2710
27
0
0
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
2 years
1
...
2659
26
0
0
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
17 months
...
2384
39
Taverna player is a rails plugin to run (...)
Robert Haines
4 weeks
4
...
2333
76
1
16
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
2320
21
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
14 months
...
2265
39
A protparam compatible utility for BioRuby (...)
hryk
19 months
1
...
2264
26
0
0
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
11 months
1
...
2223
37
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
10 months
...
2207
49
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
21 months
2
...
2169
27
0
0
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
3 years
4
...
1789
12
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
3 years
3
...
1774
11
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
2 years
1
1772
12
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
4 years
1
...
1723
7
0
0
Publish scientific results to the semantic web (...) !
Will Strinz
6 weeks
3
16
1666
53
0
3
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
4 months
...
1553
318
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
3 years
1
...
1517
15
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
2 years
1
...
1515
15
0
0
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
2 years
...
1475
15
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
2 years
2
...
1464
15
0
0
Parser to work with file formats used in (...)
Ben J Woodcroft
1 week
...
1461
164
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
2 years
3
...
1460
16
0
0
One-line summary of your gem (...)
Toshiaki Katayama
2 years
1
...
1444
13
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
2 years
2
...
1417
15
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1405
15
0
0
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
2 years
1
...
1394
13
0
0
A simple biogem that allows computation of the (...)
Ben J Woodcroft
2 years
1
...
1374
14
0
0
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
2 years
1
...
1360
15
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1248
13
0
0
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
2 years
...
1231
10
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
11 months
1
...
1195
22
0
0
Build graph with jRuby (...)
Matteo Picciolini
24 months
...
1160
14
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
23 months
1
...
1158
13
Ruby ensembl rest api (...)
Alberto Donizetti
10 months
3
1
1102
22
0
0
Generalized linear models for statsample (...)
Ankur Goel
10 months
...
1057
26
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
4 months
...
1041
52
0
0
Vcf parser (...)
Pjotr Prins
4 weeks
11
6
1008
59
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
8 weeks
...
979
63
1
31
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
18 months
...
913
15
0
0
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
6 months
...
775
23
Interface for express beta diversity (...)
Ben J. Woodcroft
6 months
...
748
29
0
0
Bio-repeatmasker (...)
Andrei Rozanski
6 months
738
26
Biostars data-mining and statistical analysis (...)
Joachim Baran
3 months
...
702
41
0
0
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
13 months
2
...
694
13
0
0
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
12 months
...
628
12
0
0
A parser for cigar format alignments (...)
Ben J Woodcroft
5 months
3
...
592
26
0
0
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
9 weeks
1
494
33
Web server for bio-samtools (...)
homonecloco
8 weeks
...
428
33
0
19
(...) pre
pre
351
2
Mine publications for gene names (...)
Pjotr Prins
4 months
...
295
15
0
0
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
4 months
2
...
242
11
0
0
!
Server for polymarker. to be used with cron (...) new
Ricardo H.  Ramirez-Gonzalez
1 week
...
237
237
5
13
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
7 weeks
...
182
20
!
Ruby inferface for kseq.h by heng li for (...) new
Fedor Gusev
1 week
...
97
94
(...) pre
pre
80
2
*) gem downloads (total & last 90 days) from rubygems.org as of 2014-07-28
**) number of commits on GitHub (last 7 days & last 90 days)