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
13 months
306
12
156711
0
8
Parser of scientific names !
Dmitry Mozzherin
9 weeks
24
3
83998
0
6
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
11 months
26
8
60892
0
0
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
3 years
15
12
55305
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
3 months
117
48
51287
0
2
Shintaro Katayama
8 months
1
41363
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
5 weeks
16
1
38203
0
28
Http requests to entrez e-utilities
Jared Ning
2 years
8
1
34925
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
3 years
14
5
32809
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
6 years
17
5
30936
0
0
Maf parser for BioRuby
Clayton Wheeler
5 years
10
36
27882
0
0
Gff3 parser for big data !
Pjotr Prins
5 years
7
2
26350
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
2 years
13
1
25720
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
2 years
3
2
24992
4
7
A biogem to submit jobs on a queue
Francesco Strozzi
4 years
5
...
24676
0
0
Interfaces with biomodel search engine !
Niall Beard
5 years
1
...
24386
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
2 years
13
3
21972
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
5 years
4
2
21309
0
0
Ruby parsering for obo files !
Matt Yoder
6 years
5
...
21243
0
9
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
3 years
10
21
18012
0
0
Data mining algorithms for jRuby
arrigonialberto86
4 years
16
3
17895
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
1 week
11
5
17709
0
8
A fast parser for fastq files
Francesco Strozzi
5 years
10
...
16897
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
4 years
14173
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
21 months
42
9
14168
0
0
Low memory sequence emitters
Pjotr Prins
3 years
11
1
13731
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
5 years
2
1
13324
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
3 years
3
...
13202
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
17 months
13004
0
0
Build genome output files
Michael Barton
4 years
7
...
12819
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
5 years
29
15
12800
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
6 years
1
...
12746
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
6 months
2
...
12415
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
4 years
4
...
12390
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
4 years
11
2
12228
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
6 years
1
...
11671
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
5 years
2
...
11506
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
6 years
4
...
11381
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
4 years
7
1
11143
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
11 months
2
...
11072
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
5 years
3
...
10889
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
5 years
8
2
10800
0
0
Parser to work with file formats used in
Ben J Woodcroft
2 years
...
10516
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
2 years
...
10481
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
17 months
1
...
10419
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
3 years
...
10148
0
1
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
5 years
3
...
9689
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
6 years
4
...
9555
0
0
A general purpose framework for scripted handling of development/stable
mjy
4 years
2
1
9552
0
2
Library for visualizing genomic regions !
Jan Aerts
1.4
9 years
22
1
9529
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
6 years
1
...
8729
0
0
Read and manipulate cd-hit clusters
George Githinji
4 years
8358
0
0
Ruby binding for samtools tabix
throwern
4 years
5
1
8180
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
6 years
4
...
8087
0
0
A plugin that allows you to parse large
robsyme
6 years
1
...
7812
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
2 years
7719
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
4 years
2
...
7610
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
6 years
12
...
7515
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
18 months
1
...
7432
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
6 years
40
5
7073
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
14 months
1
7035
0
0
Next-generation mapping of mutations
Dan MacLean
4 years
2
...
6955
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
5 years
13
19
6875
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
4 years
6813
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
5 years
1
1
6767
0
0
Publish scientific results to the semantic web !
Will Strinz
3 years
4
16
6745
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
7 weeks
16
4
6712
0
53
Ruby binding to the ucsc kent utilities
throwern
5 years
2
...
6691
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
22 months
1
...
6561
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
10 weeks
...
6452
0
7
Bioinformatics triple-store support
Pjotr Prins
5 years
4
1
6256
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
5 years
2
1
6239
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
6 years
1
...
6055
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
4 months
1
5918
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
4 years
5909
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
4 years
...
5815
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
3 years
1
...
5664
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
13 months
1
...
5622
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
6 years
1
...
5393
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
5 years
1
...
5213
0
0
A protparam compatible utility for BioRuby
hryk
4 years
2
1
5198
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
5 years
2
...
5197
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
5 years
1
...
4777
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
4 years
2
...
4630
0
0
Biostars data-mining and statistical analysis
Joachim Baran
3 years
4303
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
2 years
2
1
4087
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
8 years
5
...
4052
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
5 months
5
2
4011
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
2 years
2
1
3870
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
22 months
3
...
3844
0
0
Gggenome Ruby client
Mitsuteru Nakao
4 years
1
...
3693
0
0
Ruby ensembl rest api
Alberto Donizetti
4 years
2
...
3646
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
3 years
6
...
3537
0
0
Generalized linear models for statsample
Ankur Goel
4 years
3506
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
8 years
90
1
3364
0
0
Interface for express beta diversity
Ben J. Woodcroft
3 years
...
3312
0
0
Bio-repeatmasker
Andrei Rozanski
3 years
...
3233
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
6 years
4
...
3209
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
6 years
3
...
3191
0
0
Helper methods for reading .delta files
robsyme
2 years
...
3183
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
6 years
1
3136
0
0
A parser for cigar format alignments
Ben J Woodcroft
3 years
4
...
3106
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
9 months
3
...
3082
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
7 years
1
...
3067
0
0
Web server for bio-samtools
homonecloco
3 years
...
3012
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
6 years
1
...
2962
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
6 years
1
...
2908
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
6 years
2
...
2901
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
5 years
4
...
2873
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
6 years
...
2859
0
0
One-line summary of your gem
Toshiaki Katayama
5 years
1
...
2859
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
5 years
4
...
2824
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
5 years
1
...
2806
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
6 years
1
...
2805
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
5 years
1
...
2795
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
5 years
3
1
2793
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
5 years
1
...
2771
0
0
Build graph with jRuby
Matteo Picciolini
5 years
2655
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
16 months
...
2462
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
4 years
...
2351
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
4 years
2
...
2173
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
2 years
...
2162
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
2 years
2104
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
4 years
...
2084
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
3 years
1
...
1878
0
0
Mine publications for gene names
Pjotr Prins
3 years
1
...
1707
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
3 years
1
...
1612
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
3 years
1577
0
0
Tools to work with fasta files, indexed with
homonecloco
3 years
...
1538
0
0
Tools to manipulate blat files from the command
homonecloco
3 years
...
1512
0
5
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
2 years
...
1476
0
0
Api of picard tool
Natapol Pornputtapong
2 years
1386
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
2 years
1329
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
8 years
1323
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
2 years
...
1107
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
2 years
1106
0
0
Basic wrapper for the kallistio mapper
homonecloco
2 years
1
...
1079
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
21 months
...
920
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
20 months
...
864
0
0
Biosql plugin for BioRuby
BioRuby project
16 months
...
627
0
0
Cache gemma with loco
Pjotr Prins
6 weeks
...
412
0
24
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
5 weeks
...
198
0
6
BioRuby executables: utilities bundled with BioRuby
BioRuby project
5 weeks
...
197
0
2
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2017-10-20
**) number of commits on GitHub (last 7 days & last 90 days)