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
12 months
305
12
153620
4
8
Parser of scientific names !
Dmitry Mozzherin
4 weeks
24
3
83123
0
6
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
10 months
26
8
60329
0
0
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
3 years
15
12
54897
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
2 months
117
48
50817
0
0
Shintaro Katayama
7 months
1
40958
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
1 week
16
1
37849
6
24
Http requests to entrez e-utilities
Jared Ning
2 years
8
1
34655
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
3 years
14
5
32536
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
6 years
17
5
30750
0
0
Maf parser for BioRuby
Clayton Wheeler
5 years
10
36
27641
0
0
Gff3 parser for big data !
Pjotr Prins
5 years
7
2
26163
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
2 years
13
1
25452
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
2 years
3
2
24471
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
4 years
5
...
24454
0
0
Interfaces with biomodel search engine !
Niall Beard
5 years
1
...
24215
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
2 years
13
3
21533
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
5 years
4
2
21158
0
0
Ruby parsering for obo files !
Matt Yoder
6 years
5
...
21075
0
9
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
3 years
10
21
17842
0
0
Data mining algorithms for jRuby
arrigonialberto86
4 years
16
3
17694
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
11 months
11
5
17361
0
0
A fast parser for fastq files
Francesco Strozzi
5 years
10
...
16764
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
4 years
14061
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
20 months
43
9
13831
0
0
Low memory sequence emitters
Pjotr Prins
3 years
11
1
13614
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
5 years
2
1
13228
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
3 years
3
...
13081
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
16 months
12741
0
0
Build genome output files
Michael Barton
4 years
7
...
12736
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
6 years
1
...
12672
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
5 years
29
15
12649
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
5 months
2
...
12279
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
4 years
4
...
12277
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
4 years
11
2
11954
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
6 years
1
...
11599
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
5 years
2
...
11407
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
6 years
4
...
11299
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
4 years
7
1
11057
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
5 years
3
...
10804
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
5 years
8
2
10717
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
10 months
2
...
10647
0
0
Parser to work with file formats used in
Ben J Woodcroft
2 years
...
10367
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
2 years
...
10318
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
16 months
1
...
10103
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
3 years
...
10096
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
5 years
3
...
9600
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
6 years
4
...
9487
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
9 years
22
1
9464
0
0
A general purpose framework for scripted handling of development/stable
mjy
4 years
2
1
9336
0
2
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
6 years
1
...
8666
0
0
Read and manipulate cd-hit clusters
George Githinji
4 years
8276
0
0
Ruby binding for samtools tabix
throwern
3 years
5
1
8101
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
6 years
4
...
8017
0
0
A plugin that allows you to parse large
robsyme
6 years
1
...
7751
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
2 years
7576
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
4 years
2
...
7549
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
6 years
12
...
7463
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
17 months
1
...
7319
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
6 years
40
5
7028
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
13 months
1
6847
0
0
Next-generation mapping of mutations
Dan MacLean
4 years
2
...
6818
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
5 years
13
19
6811
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
3 years
6735
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
5 years
1
1
6700
0
0
Publish scientific results to the semantic web !
Will Strinz
3 years
3
16
6683
0
0
Ruby binding to the ucsc kent utilities
throwern
4 years
2
...
6621
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
21 months
1
...
6480
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
3 weeks
16
4
6439
0
53
Dead simple method of running shell commands from
Ben J. Woodcroft
6 weeks
...
6288
0
7
Bioinformatics triple-store support
Pjotr Prins
5 years
4
1
6195
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
5 years
2
1
6181
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
6 years
1
...
5994
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
4 years
5845
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
4 years
...
5754
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
3 months
1
5742
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
3 years
1
...
5585
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
12 months
1
...
5476
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
6 years
1
...
5346
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
5 years
1
...
5167
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
5 years
2
...
5153
0
0
A protparam compatible utility for BioRuby
hryk
4 years
2
1
5144
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
5 years
1
...
4733
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
4 years
2
...
4579
0
0
Biostars data-mining and statistical analysis
Joachim Baran
3 years
4241
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
2 years
2
1
4020
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
8 years
5
...
4002
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
4 months
5
2
3890
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
2 years
2
1
3821
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
21 months
3
...
3760
0
0
Gggenome Ruby client
Mitsuteru Nakao
4 years
1
...
3647
0
0
Ruby ensembl rest api
Alberto Donizetti
3 years
2
...
3600
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
3 years
6
...
3507
0
0
Generalized linear models for statsample
Ankur Goel
3 years
3460
0
0
Interface for express beta diversity
Ben J. Woodcroft
3 years
...
3267
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
8 years
90
1
3257
0
0
Bio-repeatmasker
Andrei Rozanski
3 years
...
3188
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
6 years
4
...
3180
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
6 years
3
...
3163
0
0
Helper methods for reading .delta files
robsyme
2 years
...
3120
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
6 years
1
3109
0
0
A parser for cigar format alignments
Ben J Woodcroft
3 years
4
...
3060
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
7 years
1
...
3043
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
8 months
3
...
3028
0
0
Web server for bio-samtools
homonecloco
3 years
...
2966
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
6 years
1
...
2934
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
6 years
1
...
2879
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
5 years
2
...
2871
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
5 years
4
...
2844
0
0
One-line summary of your gem
Toshiaki Katayama
5 years
1
...
2831
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
6 years
...
2829
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
5 years
4
...
2793
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
6 years
1
...
2783
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
5 years
1
...
2778
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
5 years
1
...
2768
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
5 years
3
1
2765
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
5 years
1
...
2743
0
0
Build graph with jRuby
Matteo Picciolini
5 years
2594
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
15 months
...
2385
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
4 years
...
2320
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
4 years
2
...
2143
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
2 years
...
2115
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
4 years
...
2056
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
2 years
2052
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
3 years
1
...
1845
0
0
Mine publications for gene names
Pjotr Prins
3 years
1
...
1678
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
2 years
1
...
1584
0
1
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
3 years
1550
0
0
Tools to work with fasta files, indexed with
homonecloco
2 years
...
1510
0
0
Tools to manipulate blat files from the command
homonecloco
2 years
...
1483
5
5
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
2 years
...
1448
0
0
Api of picard tool
Natapol Pornputtapong
2 years
1356
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
8 years
1303
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
2 years
1301
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
2 years
1075
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
24 months
...
1074
0
0
Basic wrapper for the kallistio mapper
homonecloco
23 months
1
...
1048
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
20 months
...
889
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
19 months
...
836
0
0
Biosql plugin for BioRuby
BioRuby project
15 months
...
596
0
0
Cache gemma with loco
Pjotr Prins
2 weeks
...
357
0
24
BioRuby executables: utilities bundled with BioRuby
BioRuby project
6 days
...
151
2
2
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
6 days
...
150
6
6
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2017-09-21
**) number of commits on GitHub (last 7 days & last 90 days)