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
17 months
313
13
171080
0
0
Parser of scientific names !
Dmitry Mozzherin
1 week
24
3
87988
0
3
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
5 weeks
26
9
63999
0
22
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
3 years
15
12
56957
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
8 months
122
51
54161
0
0
Shintaro Katayama
12 months
1
1
43032
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
5 months
16
1
39617
0
0
Http requests to entrez e-utilities
Jared Ning
2 years
8
1
36009
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
4 years
14
5
34165
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
6 years
17
5
31675
0
0
Maf parser for BioRuby
Clayton Wheeler
5 years
10
36
28858
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
4 weeks
27244
0
0
Gff3 parser for big data !
Pjotr Prins
5 years
7
2
27097
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
2 years
13
1
26707
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
5 years
5
...
25554
0
0
Interfaces with biomodel search engine !
Niall Beard
5 years
1
...
25350
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 years
13
3
23206
0
0
Ruby parsering for obo files !
Matt Yoder
6 years
5
...
22210
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
5 years
4
2
21840
0
0
Data mining algorithms for jRuby
arrigonialberto86
4 years
16
3
18717
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
3 years
10
21
18703
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
4 months
11
5
18508
0
0
A fast parser for fastq files
Francesco Strozzi
5 years
10
...
17439
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
2 years
45
9
15268
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
5 years
14636
0
0
Low memory sequence emitters
Pjotr Prins
3 years
11
1
14199
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
21 months
14059
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
6 years
2
1
13712
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
3 years
3
...
13660
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
5 years
29
15
13529
0
0
Build genome output files
Michael Barton
4 years
7
...
13316
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
6 years
1
...
13177
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
9 weeks
2
...
13165
0
8
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
4 years
11
2
13080
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
10 months
2
...
12976
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
4 years
4
...
12858
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
6 years
1
...
12073
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
5 years
2
...
11891
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
7 years
4
...
11710
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
21 months
1
...
11625
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
4 years
7
1
11502
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
5 years
3
...
11216
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
2 years
...
11159
0
0
Parser to work with file formats used in
Ben J Woodcroft
3 years
...
11145
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
5 years
8
3
11117
0
8
A general purpose framework for scripted handling of development/stable
mjy
4 years
2
1
10538
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
3 years
...
10338
0
2
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
5 years
3
...
10149
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
6 years
4
...
9818
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
10 years
23
1
9784
0
2
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
6 years
1
...
8970
0
0
Read and manipulate cd-hit clusters
George Githinji
4 years
8677
0
0
Ruby binding for samtools tabix
throwern
4 years
5
1
8500
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
6 years
4
...
8339
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
2 years
8268
0
0
A plugin that allows you to parse large
robsyme
6 years
1
...
8052
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
5 years
2
...
7859
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
22 months
1
...
7772
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
7 years
12
...
7750
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
5 months
17
4
7732
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
18 months
1
7565
0
0
Next-generation mapping of mutations
Dan MacLean
5 years
2
...
7317
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
7 years
40
5
7303
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
6 months
...
7168
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
4 years
7136
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
5 years
13
19
7133
0
0
Publish scientific results to the semantic web !
Will Strinz
3 years
4
16
7110
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
11 weeks
1
7040
0
5
Chembl rest api client, parser and container
Mitsuteru Nakao
5 years
1
1
7018
0
0
Ruby binding to the ucsc kent utilities
throwern
5 years
2
...
6944
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
2 years
1
...
6887
0
0
Bioinformatics triple-store support
Pjotr Prins
5 years
4
1
6509
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
6 years
2
1
6480
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
17 months
1
...
6302
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
7 years
1
...
6232
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
5 years
6149
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
4 years
...
6066
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
3 years
1
...
5986
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
6 years
1
...
5580
0
0
A protparam compatible utility for BioRuby
hryk
5 years
2
1
5463
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
6 years
1
...
5386
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
5 years
2
...
5363
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
5 years
1
...
4945
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
5 years
2
...
4823
0
0
Biostars data-mining and statistical analysis
Joachim Baran
3 years
4555
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
9 months
6
2
4520
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
8 years
5
...
4352
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
2 years
2
1
4344
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
2 years
3
...
4180
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
2 years
2
1
4053
0
0
Gggenome Ruby client
Mitsuteru Nakao
4 years
1
...
3873
0
0
Ruby ensembl rest api
Alberto Donizetti
4 years
2
...
3827
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
4 years
6
...
3704
0
0
Generalized linear models for statsample
Ankur Goel
4 years
3691
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
9 years
90
1
3668
0
0
Interface for express beta diversity
Ben J. Woodcroft
4 years
...
3487
0
0
Helper methods for reading .delta files
robsyme
2 years
...
3438
0
0
Bio-repeatmasker
Andrei Rozanski
4 years
...
3414
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
7 years
4
...
3321
0
0
A parser for cigar format alignments
Ben J Woodcroft
3 years
4
...
3298
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
13 months
3
...
3297
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
7 years
3
...
3295
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
6 years
1
3242
0
0
Web server for bio-samtools
homonecloco
3 years
...
3200
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
8 years
1
...
3176
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
6 years
1
...
3061
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
6 years
1
...
3023
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
6 years
2
...
3015
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
6 years
4
...
2984
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
6 years
...
2969
0
0
One-line summary of your gem
Toshiaki Katayama
6 years
1
...
2969
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
6 years
4
...
2940
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
6 years
1
...
2916
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
6 years
1
...
2907
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
5 years
3
1
2903
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
6 years
1
...
2894
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
6 years
1
...
2880
0
0
Build graph with jRuby
Matteo Picciolini
5 years
2811
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
20 months
...
2774
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
5 years
...
2470
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
2 years
...
2352
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
4 years
2
...
2297
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
2 years
2284
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
4 years
...
2206
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
3 years
1
...
2001
0
0
Mine publications for gene names
Pjotr Prins
3 years
1
...
1822
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
3 years
1
...
1728
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
3 years
1684
0
0
Tools to work with fasta files, indexed with
homonecloco
3 years
...
1655
0
0
Tools to manipulate blat files from the command
homonecloco
3 years
...
1619
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
3 years
...
1583
0
0
Api of picard tool
Natapol Pornputtapong
2 years
1498
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
2 years
1442
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
9 years
1430
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
2 years
...
1228
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
2 years
1219
0
0
Basic wrapper for the kallistio mapper
homonecloco
2 years
1
...
1197
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
2 years
...
1042
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
2 years
...
982
0
5
Cache gemma with loco
Pjotr Prins
1 week
...
807
0
1
Biosql plugin for BioRuby
BioRuby project
20 months
...
755
0
0
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
5 months
...
350
0
0
BioRuby executables: utilities bundled with BioRuby
BioRuby project
5 months
...
339
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2018-02-21
**) number of commits on GitHub (last 7 days & last 90 days)