biogems.info - gems for bioinformatics

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

#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library	BioRuby project	2.0.1	11 weeks	331	12	223132	0	16
2	biodiversity	Parser of scientific names	Dmitry Mozzherin	4.0.2	5 days	28	...	103417	9	9
3	bio samtools	Binder of samtools for Ruby, on the top	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.6.2	22 months	31	11	72022	0	1
4	sequenceserver	Blast search made easy!	Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.	1.0.12	3 months	175	49	65992	0	51
5	bio gem	Biogem is a software generator for Ruby in	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	5 years	14	12	61871	0	0
6	bio gadget		Shintaro Katayama	0.5.0	2 years	1	1	47832	0	0
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome	Hiroyuki Mishima, Jan Aerts	0.6.5	18 months	17	1	44082	0	0
8	bio polyploid tools	Tool to work with polyploids, ngs and molecular	Ricardo H. Ramirez-Gonzalez	1.1.1	2 weeks	1	...	39348	0	0
9	entrez	Http requests to entrez e-utilities	Jared Ning	0.5.8.2	4 years	8	1	38982	0	0
10	bio svgenes	Create pretty svg-format images of features, gene models	Dan MacLean	0.4.1	5 years	15	5	38069	0	0
11	togostanza	Development tools of togostanza	Keita Urashima	2.1.3	17 months			36282	0	0
12	biomart	A Ruby api for interacting with biomart services	Darren Oakley	0.2.3	8 years	18	5	33881	0	0
13	bio maf	Maf parser for BioRuby	Clayton Wheeler	1.0.1	7 years	10	36	31717	0	0
14	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer	Pjotr Prins	2.0.4	4 years	17	1	30496	0	0
15	bio gff3	Gff3 parser for big data	Pjotr Prins	0.9.1	7 years	7	2	29343	0	0
16	bio grid	A biogem to submit jobs on a queue	Francesco Strozzi	0.3.3	7 years	4	...	28161	0	0
17	search biomodel	Interfaces with biomodel search engine	Niall Beard	2.1.6	7 years	1	...	27776	0	0
18	biointerchange	An open source framework for transforming heterogeneous data	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	4 years	13	3	26234	0	0
19	bio logger	Log4r wrapper with extra features for roles and	Pjotr Prins	1.0.1	7 years	4	2	24872	0	0
20	obo parser	Ruby parsering for obo files	Matt Yoder	0.4.2	8 years	6	...	24498	0	0
21	bio basespace sdk	Basespace Ruby sdk is a Ruby based software	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	6 years	11	2	21126	0	0
22	bio band	Data mining algorithms for jRuby	arrigonialberto86	0.1.11	6 years	15	3	21093	0	0
23	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv	Pjotr Prins	1.0.0	5 years	9	21	20935	0	0
24	bio alignment	Support for multiple sequence alignments (msa)	Pjotr Prins	0.1.0	2 years	10	5	20737	0	0
25	bio rocker	Rocker	Luis (Coto) Orellana, Luis M. Rodriguez-R	1.5.2	3 months			19658	0	0
26	bio fastqc	Ruby parser for fastqc output	Tazro Inutano Ohta	0.10.8	16 months	2	...	19314	0	0
27	bio faster	A fast parser for fastq files	Francesco Strozzi	0.4.5	7 years	9	...	19043	0	0
28	bio vcf	Fast multi-purpose multi-threaded vcf parser	Pjotr Prins	0.9.2	3 years	57	9	18455	0	0
29	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha	George Githinji	0.7.1	6 years			15983	0	0
30	bio bigbio	Low memory sequence emitters	Pjotr Prins	0.1.6	5 years	10	1	15646	0	0
31	bio ngs	Bio-ngs provides a framework for handling ngs data	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	7 years	28	16	15213	0	0
32	bio signalp	A wrapper for the signal peptide prediction algorith	Ben J Woodcroft	0.3.1	5 years	3	1	15092	0	0
33	genevalidator	Identifying problems with gene predictions	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	2.1.5	15 months	1	...	14915	0	0
34	bio phyta	Pipeline to remove contaminations from est libraries	Philipp Comans	0.9.4	7 years	2	1	14874	0	0
35	scaffolder	Build genome output files	Michael Barton	0.5.0	6 years	7	...	14643	0	0
36	bio tm hmm	A BioRuby plugin for interaction with the transmembrane	Ben J. Woodcroft	0.2.4	2 years	2	...	14588	0	0
37	nexus parser	A nexus file format (phylogenetic inference) parser in	mjy	1.1.4	8 years	1	...	14241	0	0
38	bio kmer counter	A biogem for counting small kmers for fingerprinting	Ben J Woodcroft	0.1.2	6 years	4	...	14223	0	0
39	taxonifi	A general purpose framework for scripted handling of development/stable	mjy	0.4.0	6 years	2	1	13693	0	0
40	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor	mjy	0.2.6	8 years	1	...	13094	0	0
41	bio polymarker db batch	Server for polymarker. to be used with cron	Ricardo H. Ramirez-Gonzalez	0.5.1	4 years		...	13064	0	0
42	bio sambamba	Ruby wrapper for sambamba tool	Artem Tarasov	0.0.5	7 years	2	...	13055	0	0
43	bio velvet	Parser to work with file formats used in	Ben J Woodcroft	0.6.0	4 years		...	12982	0	0
44	bio assembly	BioRuby assembly plugin	Chase Miller, Francesco Strozzi	0.1.0	8 years	4	...	12687	0	0
45	bio bgzf	Reading/writing bgzf blocks	Artem Tarasov, Clayton Wheeler	0.2.1	7 years	3	...	12543	0	0
46	eutils	Lightweight Ruby api for ncbi eutils	Joon Lee, aka seouri	0.2.1	6 years	7	1	12438	0	0
47	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point	George Githinji, Pascal Betz	0.1.3	7 years			12231	0	0
48	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org)	Rutger Vos, Anurag Priyam	1.1.0	7 years	8	3	12063	0	0
49	genevalidatorapp	A web app wrapper for genevalidator	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	2.1.7	14 months	1	...	11327	0	0
50	bioportal	Supports linking of models within a ror application	Stuart Owen, Quyen Nguyen	2.2	5 years		...	10884	0	0
51	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps	Hiroyuki Mishima	0.1.2	8 years	4	...	10695	0	0
52	ref2bibtex	Pass a full citation, get the bibtex back,	Matt Yoder	0.3.0	8 months		1	10565	0	0
53	bio graphics	Library for visualizing genomic regions	Jan Aerts	1.4	11 years	22	2	10552	0	0
54	bio pipengine	A pipeline manager	Francesco Strozzi, Raoul Jean Pierre Bonnal	0.9.7	2 years	18	4	10309	0	0
55	bio fasta retrieve	Retrieve dna sequence from ucsc using given coordinates	Andrei Rozanski	0.0.7	4 years			9834	0	0
56	bio octopus	Running and parsing of the protein transmembrane domain	Ben J Woodcroft	0.1.1	8 years	1	...	9721	0	0
57	bio cd hit report	Read and manipulate cd-hit clusters	George Githinji	0.1.0	6 years			9682	0	0
58	bio tabix	Ruby binding for samtools tabix	throwern	1.0.1	6 years	5	1	9441	0	0
59	bio commandeer	Dead simple method of running shell commands from	Ben J. Woodcroft	0.4.0	2 years		...	9124	0	0
60	bio bwa	Ruby binding for bwa mapping software	Francesco Strozzi	0.2.2	8 years	4	...	9113	0	0
61	bio velvet underground	Bindings to some internals of the velvet assembler	Ben Woodcroft	0.3.1	3 years		1	8944	0	0
62	bio lazyblastxml	A plugin that allows you to parse large	robsyme	0.4.0	8 years	1	...	8771	0	0
63	bio plasmoap	Implementation of the plasmoap algorithm	Ben J Woodcroft	0.1.1	3 years	1	...	8752	0	0
64	bio pileup iterator	Iterate through a samtools pileup file	Ben J. Woodcroft	0.0.4	7 years	2	...	8611	0	0
65	goruby	Gene ontology (go) interface for Ruby	Ben J Woodcroft	0.2.0	9 years	12	...	8361	0	0
66	bio gngm	Next-generation mapping of mutations	Dan MacLean	0.2.1	6 years	2	...	8093	0	0
67	bio statsample timeseries	Timeseries modules for statsample	Ankur Goel, Claudio Bustos	0.2.1	6 years			8084	0	0
68	publisci	Publish scientific results to the semantic web	Will Strinz	0.1.6	5 years	4	16	8057	0	0
69	ruby ensembl api	Api to ensembl databases	Jan Aerts, Francesco Strozzi	1.0.1	8 years	41	5	7955	0	0
70	bio gff3 pltools	Ruby wrapper for the gff3-pltools	Marjan Povolni	0.3.0	7 years	15	19	7890	0	0
71	bio krona	This biogem is built around krona, a flashy	Ben J. Woodcroft	0.2.0	3 years	1	...	7848	0	0
72	bio chembl	Chembl rest api client, parser and container	Mitsuteru Nakao	0.1.3	7 years	1	1	7769	0	0
73	bio ucsc util	Ruby binding to the ucsc kent utilities	throwern	0.1.2	7 years	2	...	7711	0	0
74	bio rdf	Bioinformatics triple-store support	Pjotr Prins	0.0.2	7 years	4	1	7214	0	0
75	bio affy	Parse affymetrix cel/cdf files	Pjotr Prins	0.5.1	7 years	2	1	7165	0	0
76	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)	Andrei Rozanski	1.3.0	5 years	1	...	6902	0	0
77	bio unichem	BioRuby plugin for unichem rest web service	Mitsuteru Nakao	0.3.0	6 years			6902	0	0
78	bio synreport	Reports whether a nucleotide change results in synonymous	Dan MacLean	0.1.2	6 years		...	6814	0	0
79	bio kb illumina	Geneexpression illuminahumanannotation	Raoul J.P. Bonnal	0.1.0	8 years	1	...	6762	0	0
80	bio protparam	A protparam compatible utility for BioRuby	hryk	0.2.0	6 years	2	1	6431	0	0
81	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser,	Raoul J.P. Bonnal	0.0.1	8 years	1	...	6133	0	0
82	ncbi blast dbs	Fast download blast databases from ncbi beta	Anurag Priyam	0.0.6	2 years	14	4	6097	0	0
83	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be	Ben J Woodcroft	0.0.3	7 years	1	...	5917	0	0
84	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal	Ben J. Woodcroft	0.3.0	7 years	2	...	5900	0	0
85	bio hmmer model	Parse pfam hmm definition files	Ben J. Woodcroft	0.0.2	7 years	1	...	5479	0	0
86	bio gag	Bio-gag is a biogem for detecting and correcting	Ben J Woodcroft	0.1.0	7 years	2	...	5391	0	0
87	bio biostars analytics	Biostars data-mining and statistical analysis	Joachim Baran	0.2.0	5 years			5297	0	0
88	bio sra	A sequence read archive (sra) download script and	Ben J. Woodcroft	0.3.1	3 years	4	...	5113	0	0
89	bio locus	Fast storage and comparison of chr+pos(+alt) locations	Pjotr Prins	0.0.7	4 years	2	1	5108	0	0
90	nbio cloudquery	Client for xoopit's cloudquery api	Cameron Walters, nb.io	0.1.5	10 years	5	...	5085	0	0
91	rubyBHL	Rubybhl is a simple request/response wrapper for the	Matt Yoder	0.3.1	7 weeks	6	...	4860	0	4
92	bio hmmer3 report	Enables parsing of hmmer version 3 reports	Christian Zmasek, Ben J Woodcroft	0.1.0	4 years	2	1	4629	0	0
93	bio gggenome	Gggenome Ruby client	Mitsuteru Nakao	0.2.0	6 years	1	...	4411	0	0
94	bio ensembl rest	Ruby ensembl rest api	Alberto Donizetti	0.2.0	6 years	2	...	4361	0	0
95	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a	Cameron Walters, Randy Reddig	1.0.3	10 years	89	1	4346	0	0
96	bio statsample glm	Generalized linear models for statsample	Ankur Goel	0.1.1	6 years			4259	0	0
97	bio mummer	Helper methods for reading .delta files	robsyme	0.2.1	4 years		...	4169	0	0
98	bio express beta diversity	Interface for express beta diversity	Ben J. Woodcroft	0.1.0	5 years		...	4030	0	0
99	bio repeatmasker	Bio-repeatmasker	Andrei Rozanski	0.0.3	5 years	1	...	3958	0	0
100	bio ipcress	A programmatic interface to the ipcress in-silico pcr	Ben J Woodcroft	0.1.0	2 years	3	...	3928	0	0
101	bio cigar	A parser for cigar format alignments	Ben J Woodcroft	0.1.0	5 years	4	...	3841	0	0
102	bio samtools server	Web server for bio-samtools	homonecloco	0.1.2	5 years		...	3726	0	0
103	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives	Naohisa Goto	1.0.0	3 years		...	3719	0	0
104	bio sge	BioRuby plugin for sun grid engine	Toshiaki Katayama	0.0.0	8 years	4	...	3705	0	0
105	bio hello	Hello world plugin for the BioRuby (just for	Toshiaki Katayama	0.0.0	8 years	3	...	3634	0	0
106	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns	Trevor Wennblom	1.0.0	8 years		1	3579	0	0
107	dna sequence aligner	Does high pairwise alignment of sequencing reads with	John T. Prince	0.0.2	9 years	1	...	3499	0	0
108	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of	Ben J Woodcroft	0.1.0	8 years	1	...	3398	0	0
109	bio core ext	BioRuby core ext: plugins which require external library	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	8 years	1	...	3366	0	0
110	bio biolinux	Meta package for biolinux distribution	Raoul J.P. Bonnal	0.1.0	8 years	2	...	3354	0	0
111	bio ensembl	A Ruby api to the ensembl database	Jan Aerts, Francesco Strozzi	1.1.0	7 years	4	...	3337	0	0
112	bio data restriction enzyme	Restriction enzyme dataset	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	8 years		...	3323	0	0
113	bio foo	One-line summary of your gem	Toshiaki Katayama	0.0.0	8 years	1	...	3309	0	0
114	bio dbsnp	Decoding the dbsnp bitfield	Hiroyuki Mishima	0.1.1	8 years	4	...	3296	0	0
115	bio hydropathy	Hydropathy scale for BioRuby	Ben J Woodcroft	0.0.1	7 years	1	...	3260	0	0
116	bio phyloxml	Phyloxml plugin for BioRuby	Diana Jaunzeikare, Clayton Wheeler	0.9.0	7 years	3	1	3228	0	0
117	bio exportpred	Wrapper around the exportpred algorithm for predicting p	Ben J Woodcroft	0.0.1	7 years	1	...	3225	0	0
118	bio aliphatic index	A simple biogem that allows computation of the	Ben J Woodcroft	0.0.1	7 years	1	...	3224	0	0
119	intermine bio	Biological extensions for the intermine webservice client library	Alex Kalderimis	0.98.1	8 years	1	...	3206	0	0
120	bio incanter	Build graph with jRuby	Matteo Picciolini	0.1.0	7 years			3159	0	0
121	bio gfastqc	Aggregate fastqc (quality control for next generation sequencing	Raoul Jean Pierre Bonnal	0.0.4	4 years		...	2884	0	0
122	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata	Ben J. Woodcroft	0.0.1	6 years		...	2833	0	0
123	bio freebayes	The api for freebayes version #{bio::freebayes::extversion}	Natapol Pornputtapong	0.1.6	4 years			2824	0	0
124	bio stockholm	Parse stockholm sequence alignment format	Ben J. Woodcroft	0.0.1	6 years	2	...	2679	0	0
125	bio gemma wrapper	gemma with loco and permutations	Pjotr Prins	0.98.1	12 months		...	2621	0	0
126	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood	Fernando Izquierdo	0.1.0	6 years		...	2556	0	0
127	bio kseq	Ruby inferface for kseq.h by heng li for	Fedor Gusev	0.0.2	5 years	1	...	2379	0	0
128	bio exominer	Mine publications for gene names	Pjotr Prins	0.0.3	5 years	2	...	2162	0	0
129	bark	A Ruby wrapper on the open tree api beta	Matt Yoder	0.0.2	5 years	1	...	2084	0	0
130	bio faidx	Tools to work with fasta files, indexed with	homonecloco	0.0.1	5 years		...	2009	0	0
131	genomichdt	A restful service for sharing genomic data	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	5 years			1978	0	0
132	bio blat tools	Tools to manipulate blat files from the command	homonecloco	0.1.0	5 years		...	1971	0	0
133	bio location rdfize	Faldo location output method for bio::location in BioRuby	Joachim Baran, Naohisa Goto	0.0.0	5 years		...	1928	0	0
134	bio picard	Api of picard tool	Natapol Pornputtapong	1.131.5	4 years			1843	0	0
135	bio sparql client	A Ruby wrapper for bio sparql service	Natapol Pornputtapong	0.0.1	4 years			1793	0	0
136	nbio css http request	Csshttprequest is cross-domain ajax using css disabled	Cameron Walters, Randy Reddig	0.1	10 years			1714	0	0
137	bio kallisto	Basic wrapper for the kallistio mapper	homonecloco	0.1.0	4 years	1	...	1572	0	0
138	bio jaspar	Tools for jaspar motifs in BioRuby	Jessica Lee, Wasserman Lab	0.1.0	4 years		...	1565	0	0
139	bio conduit	A pipeline creator for BioRuby	Natapol Pornputtapong	1.0.0	4 years			1561	0	0
140	bio plates	Methods for handling multiwell plate annotations	Steve Pettitt	0.2.0	3 years		...	1376	0	0
141	bio sam mutation	Parsing and mutation calling from sam, cigar and	Stephen Pettitt	0.4.1	3 years		1	1309	0	0
142	bio shell	BioRuby shell: interactive analysis environment for BioRuby	BioRuby project	1.0.0	5 months		...	1264	0	0
143	bio executables	BioRuby executables: utilities bundled with BioRuby	BioRuby project	1.0.0	5 months		...	1219	0	0
144	bio biosql	Biosql plugin for BioRuby	BioRuby project	0.0.0	3 years		...	1106	0	0
145	bio blast seq extract	Extract the sequence of the subjects' region based	Sishuo Wang	0.2.2	3 months			626	0	0
146	bio blast xmlparser	BioRuby blast xmlparser plugin	BioRuby project	0.0.0	5 months		...	544	0	0
147	bio iqtree	Iq-tree analysis with Ruby	evolbeginner	0.1.2	3 months			494	0	0
148	bio primer3	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)