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
325
13
198520
3
8
Parser of scientific names !
Dmitry Mozzherin
2 months
26
4
94574
0
1
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
11 months
29
10
67920
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
17 months
135
42
59204
0
13
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
4 years
14
12
59169
0
0
Shintaro Katayama
22 months
1
1
45245
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
7 months
17
1
41787
0
0
Http requests to entrez e-utilities
Jared Ning
3 years
8
1
37346
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
4 years
15
5
36033
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
2 weeks
32860
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
7 years
17
5
32695
0
0
Maf parser for BioRuby
Clayton Wheeler
6 years
10
36
30191
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
3 years
14
1
28951
0
0
Gff3 parser for big data !
Pjotr Prins
6 years
7
2
28111
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
6 years
4
...
26722
0
0
Interfaces with biomodel search engine !
Niall Beard
6 years
1
...
26391
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 years
13
3
24580
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
6 years
4
2
23694
0
0
Ruby parsering for obo files !
Matt Yoder
7 years
5
...
23190
0
0
Data mining algorithms for jRuby
arrigonialberto86
5 years
16
3
19799
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
4 years
8
21
19633
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
14 months
11
5
19532
0
0
A fast parser for fastq files
Francesco Strozzi
6 years
9
...
18162
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
2 years
54
9
16853
0
3
Ruby parser for fastqc output
Tazro Inutano Ohta
4 months
2
...
16295
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
5 months
15632
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
5 years
11
2
15391
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
5 years
15245
0
0
Low memory sequence emitters
Pjotr Prins
4 years
10
1
14838
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
4 years
3
...
14311
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
7 years
2
1
14237
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
6 years
27
15
14233
0
0
Build genome output files
Michael Barton
5 years
7
...
13878
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
20 months
2
...
13727
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
7 years
1
...
13627
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
5 years
4
...
13487
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
3 months
1
...
13273
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
7 years
1
...
12490
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
6 years
2
...
12415
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
7 years
4
...
12153
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
3 years
...
12045
0
0
Parser to work with file formats used in
Ben J Woodcroft
3 years
...
12000
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
5 years
7
1
11907
0
0
A general purpose framework for scripted handling of development/stable
mjy
5 years
2
1
11824
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
6 years
11684
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
6 years
8
3
11541
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
6 years
3
...
11093
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
4 years
...
10600
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
7 years
4
...
10209
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
10 years
23
1
10130
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
3 months
1
...
9481
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
7 years
1
...
9311
0
0
Read and manipulate cd-hit clusters
George Githinji
5 years
9158
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
3 years
8993
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
15 months
17
4
8944
0
0
Ruby binding for samtools tabix
throwern
5 years
5
1
8935
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
7 years
4
...
8692
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
9 months
1
8556
0
1
A plugin that allows you to parse large
robsyme
7 years
1
...
8372
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
2 years
1
8218
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
2 years
1
...
8211
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
6 years
2
...
8197
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
16 months
...
8099
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
8 years
12
...
8003
0
0
Next-generation mapping of mutations
Dan MacLean
6 years
2
...
7664
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
7 years
40
5
7578
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
5 years
7570
0
0
Publish scientific results to the semantic web !
Will Strinz
4 years
4
16
7528
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
6 years
15
19
7475
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
6 years
1
1
7353
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
3 years
1
...
7321
0
0
Ruby binding to the ucsc kent utilities
throwern
6 years
2
...
7302
0
0
Bioinformatics triple-store support
Pjotr Prins
6 years
4
1
6816
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
7 years
2
1
6788
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
5 years
6481
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
7 years
1
...
6466
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
4 years
1
...
6412
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
5 years
...
6398
0
0
A protparam compatible utility for BioRuby
hryk
5 years
2
1
5993
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
7 years
1
...
5833
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
6 years
1
...
5630
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
6 years
2
...
5604
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
19 months
11
3
5323
0
2
Parse pfam hmm definition files
Ben J. Woodcroft
6 years
1
...
5182
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
6 years
2
...
5069
0
0
Biostars data-mining and statistical analysis
Joachim Baran
4 years
4888
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
3 years
2
1
4687
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
9 years
5
...
4660
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
2 years
3
...
4609
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
3 years
2
1
4315
0
0
Gggenome Ruby client
Mitsuteru Nakao
5 years
1
...
4113
0
0
Ruby ensembl rest api
Alberto Donizetti
5 years
2
...
4069
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
9 years
91
1
3957
0
0
Generalized linear models for statsample
Ankur Goel
5 years
3952
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
4 years
6
...
3899
0
0
Helper methods for reading .delta files
robsyme
3 years
...
3772
0
0
Interface for express beta diversity
Ben J. Woodcroft
4 years
...
3732
0
0
Bio-repeatmasker
Andrei Rozanski
4 years
1
...
3664
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
23 months
3
...
3591
0
0
A parser for cigar format alignments
Ben J Woodcroft
4 years
4
...
3546
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
7 years
4
...
3493
0
0
Web server for bio-samtools
homonecloco
4 years
...
3443
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
7 years
3
...
3438
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
7 years
1
3385
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
2 years
...
3337
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
8 years
1
...
3317
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
7 years
1
...
3211
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
7 years
1
...
3175
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
7 years
2
...
3170
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
7 years
...
3128
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
7 years
4
...
3128
0
0
One-line summary of your gem
Toshiaki Katayama
7 years
1
...
3122
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
7 years
4
...
3099
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
6 years
1
...
3066
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
6 years
3
1
3046
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
6 years
1
...
3042
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
7 years
1
...
3037
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
6 years
1
...
3035
0
0
Build graph with jRuby
Matteo Picciolini
6 years
2965
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
5 years
...
2628
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
3 years
...
2592
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
3 years
2529
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
5 years
2
...
2473
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
5 years
...
2361
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
4 years
1
...
2167
0
0
Mine publications for gene names
Pjotr Prins
4 years
2
...
1971
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
4 years
1
...
1883
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
4 years
1812
0
0
Tools to work with fasta files, indexed with
homonecloco
4 years
...
1805
0
0
gemma with loco and permutations
Pjotr Prins
3 weeks
...
1779
1
7
Tools to manipulate blat files from the command
homonecloco
4 years
...
1772
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
4 years
...
1737
0
0
Api of picard tool
Natapol Pornputtapong
3 years
1653
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
3 years
1597
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
9 years
1549
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
3 years
...
1377
0
0
Basic wrapper for the kallistio mapper
homonecloco
3 years
1
...
1371
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
3 years
1367
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
2 years
...
1191
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
2 years
1
1131
0
0
Biosql plugin for BioRuby
BioRuby project
2 years
...
915
0
0
BioRuby shell: interactive analysis environment for BioRuby
BioRuby project
15 months
...
511
0
0
BioRuby executables: utilities bundled with BioRuby
BioRuby project
15 months
...
504
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2018-12-11
**) number of commits on GitHub (last 7 days & last 90 days)