Matsumoto Yukihiro, a.k.a. Matz, visits Biohackathon 2018 !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
11 weeks
331
12
223132
0
16
Parser of scientific names !
Dmitry Mozzherin
5 days
28
...
103417
9
9
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
22 months
31
11
72022
0
1
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
3 months
175
49
65992
0
51
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
5 years
14
12
61871
0
0
Shintaro Katayama
2 years
1
1
47832
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
18 months
17
1
44082
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
2 weeks
1
...
39348
0
0
Http requests to entrez e-utilities
Jared Ning
4 years
8
1
38982
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
5 years
15
5
38069
0
0
Development tools of togostanza
Keita Urashima
17 months
36282
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
8 years
18
5
33881
0
0
Maf parser for BioRuby
Clayton Wheeler
7 years
10
36
31717
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
4 years
17
1
30496
0
0
Gff3 parser for big data !
Pjotr Prins
7 years
7
2
29343
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
7 years
4
...
28161
0
0
Interfaces with biomodel search engine !
Niall Beard
7 years
1
...
27776
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
4 years
13
3
26234
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
7 years
4
2
24872
0
0
Ruby parsering for obo files !
Matt Yoder
8 years
6
...
24498
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
6 years
11
2
21126
0
0
Data mining algorithms for jRuby
arrigonialberto86
6 years
15
3
21093
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
5 years
9
21
20935
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
2 years
10
5
20737
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
3 months
19658
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
16 months
2
...
19314
0
0
A fast parser for fastq files
Francesco Strozzi
7 years
9
...
19043
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
3 years
57
9
18455
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
6 years
15983
0
0
Low memory sequence emitters
Pjotr Prins
5 years
10
1
15646
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
7 years
28
16
15213
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
5 years
3
1
15092
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
15 months
1
...
14915
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
7 years
2
1
14874
0
0
Build genome output files
Michael Barton
6 years
7
...
14643
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
2 years
2
...
14588
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
8 years
1
...
14241
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
6 years
4
...
14223
0
0
A general purpose framework for scripted handling of development/stable
mjy
6 years
2
1
13693
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
8 years
1
...
13094
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
4 years
...
13064
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
7 years
2
...
13055
0
0
Parser to work with file formats used in
Ben J Woodcroft
4 years
...
12982
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
8 years
4
...
12687
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
7 years
3
...
12543
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
6 years
7
1
12438
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
7 years
12231
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
7 years
8
3
12063
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
14 months
1
...
11327
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
5 years
...
10884
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
8 years
4
...
10695
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
8 months
1
10565
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
11 years
22
2
10552
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
2 years
18
4
10309
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
4 years
9834
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
8 years
1
...
9721
0
0
Read and manipulate cd-hit clusters
George Githinji
6 years
9682
0
0
Ruby binding for samtools tabix
throwern
6 years
5
1
9441
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
2 years
...
9124
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
8 years
4
...
9113
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
3 years
1
8944
0
0
A plugin that allows you to parse large
robsyme
8 years
1
...
8771
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
3 years
1
...
8752
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
7 years
2
...
8611
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
9 years
12
...
8361
0
0
Next-generation mapping of mutations
Dan MacLean
6 years
2
...
8093
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
6 years
8084
0
0
Publish scientific results to the semantic web !
Will Strinz
5 years
4
16
8057
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
8 years
41
5
7955
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
7 years
15
19
7890
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
3 years
1
...
7848
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
7 years
1
1
7769
0
0
Ruby binding to the ucsc kent utilities
throwern
7 years
2
...
7711
0
0
Bioinformatics triple-store support
Pjotr Prins
7 years
4
1
7214
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
7 years
2
1
7165
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
5 years
1
...
6902
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
6 years
6902
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
6 years
...
6814
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
8 years
1
...
6762
0
0
A protparam compatible utility for BioRuby
hryk
6 years
2
1
6431
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
8 years
1
...
6133
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
2 years
14
4
6097
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
7 years
1
...
5917
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
7 years
2
...
5900
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
7 years
1
...
5479
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
7 years
2
...
5391
0
0
Biostars data-mining and statistical analysis
Joachim Baran
5 years
5297
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
3 years
4
...
5113
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
4 years
2
1
5108
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
10 years
5
...
5085
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
7 weeks
6
...
4860
0
4
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
4 years
2
1
4629
0
0
Gggenome Ruby client
Mitsuteru Nakao
6 years
1
...
4411
0
0
Ruby ensembl rest api
Alberto Donizetti
6 years
2
...
4361
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
10 years
89
1
4346
0
0
Generalized linear models for statsample
Ankur Goel
6 years
4259
0
0
Helper methods for reading .delta files
robsyme
4 years
...
4169
0
0
Interface for express beta diversity
Ben J. Woodcroft
5 years
...
4030
0
0
Bio-repeatmasker
Andrei Rozanski
5 years
1
...
3958
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
2 years
3
...
3928
0
0
A parser for cigar format alignments
Ben J Woodcroft
5 years
4
...
3841
0
0
Web server for bio-samtools
homonecloco
5 years
...
3726
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
3 years
...
3719
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
8 years
4
...
3705
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
8 years
3
...
3634
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
8 years
1
3579
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
9 years
1
...
3499
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
8 years
1
...
3398
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
8 years
1
...
3366
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
8 years
2
...
3354
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
7 years
4
...
3337
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
8 years
...
3323
0
0
One-line summary of your gem
Toshiaki Katayama
8 years
1
...
3309
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
8 years
4
...
3296
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
7 years
1
...
3260
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
7 years
3
1
3228
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
7 years
1
...
3225
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
7 years
1
...
3224
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
8 years
1
...
3206
0
0
Build graph with jRuby
Matteo Picciolini
7 years
3159
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
4 years
...
2884
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
6 years
...
2833
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
4 years
2824
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
6 years
2
...
2679
0
0
gemma with loco and permutations
Pjotr Prins
12 months
...
2621
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
6 years
...
2556
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
5 years
1
...
2379
0
0
Mine publications for gene names
Pjotr Prins
5 years
2
...
2162
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
5 years
1
...
2084
0
0
Tools to work with fasta files, indexed with
homonecloco
5 years
...
2009
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
5 years
1978
0
0
Tools to manipulate blat files from the command
homonecloco
5 years
...
1971
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
5 years
...
1928
0
0
Api of picard tool
Natapol Pornputtapong
4 years
1843
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
4 years
1793
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
10 years
1714
0
0
Basic wrapper for the kallistio mapper
homonecloco
4 years
1
...
1572
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
4 years
...
1565
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
4 years
1561
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
3 years
...
1376
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
3 years
1
1309
0
0
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
5 months
...
1264
0
0
BioRuby executables: utilities bundled with BioRuby
BioRuby project
5 months
...
1219
0
0
Biosql plugin for BioRuby
BioRuby project
3 years
...
1106
0
0
Extract the sequence of the subjects' region based
Sishuo Wang
3 months
626
0
0
BioRuby blast xmlparser plugin
BioRuby project
5 months
...
544
0
0
Iq-tree analysis with Ruby
evolbeginner
3 months
494
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2019-11-23
**) number of commits on GitHub (last 7 days & last 90 days)