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
10 months
288
12
114302
0
0
Parser of scientific names !
Dmitry Mozzherin
8 months
21
3
67799
0
0
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
10 months
23
8
50078
0
0
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
23 months
15
12
47578
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
6 weeks
88
53
37068
0
24
Gadgets for bioinformatics
Shintaro Katayama
2 years
1
33694
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
2 years
16
1
32067
0
0
Http requests to entrez e-utilities
Jared Ning
12 months
6
1
29971
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
2 years
11
5
27478
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
4 years
18
5
27370
0
0
Maf parser for BioRuby
Clayton Wheeler
3 years
10
36
23413
0
0
Gff3 parser for big data !
Pjotr Prins
3 years
6
2
22871
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
12 months
12
1
20950
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
3 years
5
...
20609
0
0
Interfaces with biomodel search engine !
Niall Beard
4 years
1
...
20378
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
4 years
4
2
18489
0
0
A simple obo file handler !
mjy
4 years
5
...
17517
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
8 months
2
1
17317
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
16 months
12
3
16776
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
23 months
9
20
14828
0
0
A fast parser for fastq files
Francesco Strozzi
3 years
10
...
14350
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
23 months
8
5
14349
0
0
Data mining algorithms for jRuby
arrigonialberto86
2 years
15
3
14155
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
3 years
12068
0
0
Low memory sequence emitters
Pjotr Prins
23 months
11
1
11597
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
4 years
2
1
11522
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
21 months
3
...
11062
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
5 years
1
...
10927
0
0
Build genome output files
Michael Barton
2 years
5
...
10710
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
2 years
5
...
10245
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
3 years
2
...
10062
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
4 years
1
...
9902
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
5 years
4
...
9895
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
15
9892
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
3 years
2
...
9718
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
2 years
8
...
9518
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
3 months
31
8
9470
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
3 years
8
2
9351
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
4 years
3
...
9319
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
2 years
...
9117
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
2 years
13
2
8373
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
8 years
22
1
8329
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
5 years
4
...
8290
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
5 months
8149
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
3 years
3
...
7922
0
0
Parser to work with file formats used in
Ben J Woodcroft
15 months
...
7674
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
5 years
1
...
7578
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
14 months
...
7388
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
5 years
4
...
6925
0
0
Read and manipulate cd-hit clusters
George Githinji
3 years
6877
0
0
Ruby binding for samtools tabix
throwern
2 years
5
...
6686
0
0
A plugin that allows you to parse large
robsyme
4 years
1
...
6680
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
5 years
10
...
6521
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
3 years
2
...
6463
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
5 years
41
5
6046
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
3 years
13
19
5706
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
3 years
1
1
5607
0
0
Next-generation mapping of mutations
Dan MacLean
3 years
2
...
5574
0
0
A general purpose framework for scripted handling of development/stable
mjy
3 years
2
1
5560
0
1
Ruby binding to the ucsc kent utilities
throwern
3 years
2
...
5553
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
2 years
5352
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
2 weeks
1
...
5336
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
8 months
5283
0
0
Publish scientific results to the semantic web !
Will Strinz
23 months
3
16
5191
0
0
Bioinformatics triple-store support
Pjotr Prins
3 years
4
1
5172
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
5 years
1
...
5152
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
4 years
2
1
5142
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
4 months
1
...
5040
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
3 years
4773
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
6 weeks
...
4720
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
2 years
...
4669
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
4 years
1
...
4555
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
15 months
1
4547
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
3 years
2
...
4377
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
4 years
1
...
4358
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
2 years
1
...
4202
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
3 years
1
...
3983
0
0
A protparam compatible utility for BioRuby
hryk
3 years
2
...
3915
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
3 years
2
...
3813
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
1 week
...
3569
0
2
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
7 months
...
3391
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
18 months
1
3206
0
0
Biostars data-mining and statistical analysis
Joachim Baran
2 years
3171
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
4 weeks
2
...
3050
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
8 months
2
1
3038
0
0
Gggenome Ruby client
Mitsuteru Nakao
2 years
1
...
2868
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
6 years
5
...
2810
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
2 years
6
...
2807
0
0
Ruby ensembl rest api
Alberto Donizetti
2 years
3
...
2803
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
5 years
3
...
2700
0
0
Generalized linear models for statsample
Ankur Goel
2 years
2691
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
5 years
4
...
2687
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
4 years
1
2660
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
6 years
1
...
2585
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
7 months
2
1
2578
0
0
Interface for express beta diversity
Ben J. Woodcroft
2 years
...
2481
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
5 years
1
...
2463
0
0
Bio-repeatmasker
Andrei Rozanski
2 years
...
2423
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
4 years
1
...
2405
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
4 years
2
...
2390
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
4 years
4
...
2380
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
4 years
...
2373
0
0
One-line summary of your gem
Toshiaki Katayama
4 years
1
...
2355
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
4 months
2
...
2346
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
4 years
1
...
2344
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
4 years
4
...
2333
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
4 years
1
...
2311
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
3 years
3
1
2310
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
4 years
1
...
2296
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
4 years
1
...
2277
0
0
A parser for cigar format alignments
Ben J Woodcroft
2 years
4
...
2276
0
0
Web server for bio-samtools
homonecloco
23 months
...
2191
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
3 years
3
...
2133
0
0
Build graph with jRuby
Matteo Picciolini
3 years
2115
0
0
Helper methods for reading .delta files
robsyme
13 months
...
2035
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
7 years
88
1
1954
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
4 days
12
7
1897
7
13
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
3 years
...
1850
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
2 years
2
...
1662
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
2 years
...
1582
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
10 weeks
2
...
1491
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
10 months
...
1330
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
11 months
1283
0
0
Mine publications for gene names
Pjotr Prins
2 years
...
1217
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
21 months
1
...
1128
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
2 years
1111
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
19 months
1
...
1079
0
0
Tools to work with fasta files, indexed with
homonecloco
19 months
...
1026
0
0
Tools to manipulate blat files from the command
homonecloco
19 months
...
1004
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
17 months
...
973
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
17 months
...
967
0
0
Api of picard tool
Natapol Pornputtapong
11 months
883
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
7 years
866
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
8 months
592
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
7 months
...
572
0
0
Basic wrapper for the kallistio mapper
homonecloco
6 months
1
...
555
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
3 months
...
392
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
12 months
370
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
11 weeks
...
332
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2016-05-01
**) number of commits on GitHub (last 7 days & last 90 days)