biogems.info

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	90d*)	7d	90d**)
								downloads		commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	3 weeks		...	42387	5296	0	82
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.1	1 day	9	5	21637	2573	8	20
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.4	14 months		...	18911	2285
4	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	0.6.0	6 months	13	3	14663	1907	0	0
5	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	22 months	4	...	12576	1484	0	0
6	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.5.2	6 months		...	10846	1406	0	0
7	intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis	1.01.00	3 months			10059	1320
8	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	10 months		...	10022	1118	0	0
9	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.5	7 weeks		...	8555	1432
10	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	14 months		...	7605	659	0	0
11	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	10 months	9	29	6985	1421	0	0
12	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	1 week		...	5718	2829
13	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	7 months		...	5537	1270	0	0
14	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	4 months	10	...	5472	686
15	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	12 months	8	...	5118	786	0	0
16	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	18 months		...	5040	533
17	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.7	11 months		4	4851	689	0	1
18	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	2 years		...	4538	453	0	0
19	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	3 years			4503	378
20	scaffolder	Genome scaffolding for human beings (...)	Michael Barton	0.4.4	22 months		...	4462	429
21	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	3 months	1	...	4332	666	0	8
22	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	5 years			4193	345
23	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	13 months		...	4142	442
24	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.5	6 weeks	6	1	4043	595	0	21
25	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.0	2 years		...	3903	389	0	0
26	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	15 months		...	3864	461
27	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	10 months		...	3690	545	0	0
28	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	2 years	3	...	3685	395	0	0
29	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	0.8.0	7 months		...	3663	758	0	0
30	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.3.3	1 week	1	5	3590	1435	0	10
31	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	2 years	1	...	3582	338
32	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	6 months		...	3570	535
33	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	12 months		...	3490	372	0	9
34	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	2 years	7	...	3266	279	0	0
35	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	10 months		...	3246	552
36	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	2 years	30	4	3084	255	0	0
37	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	2 years		...	2824	342	0	0
38	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	2 years	1	...	2696	338	0	0
39	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	2 weeks		...	2489	724	0	4
40	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	7 months	1	...	2461	349
41	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	2 years	1	...	2331	232	0	0
42	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	17 months		...	2306	220	0	0
43	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	10 months		...	2236	454	0	0
44	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	13 months	4	1	1979	239
45	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	18 months	2	1	1908	247	0	0
46	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.0	1 week		...	1813	883	1	62
47	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	21 months		...	1801	217	0	0
48	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	10 months			1672	341
49	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	13 months		...	1653	224
50	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	11 months		...	1632	318
51	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	17 months	1	...	1597	217	0	0
52	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	7 weeks		...	1589	508
53	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	6 months	1	...	1563	357	0	0
54	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	8 months		...	1534	352
55	bio tabix	Ruby binding for samtools tabix (...)	throwern	0.1.3	13 months		...	1319	223
56	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	13 months	1	...	1274	231	0	0
57	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	21 months		1	1215	111	0	0
58	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	3 years			1208	101
59	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	2 years	4	...	1203	129	0	0
60	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	2 years		...	1194	129	0	0
61	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	7 months		...	1078	230
62	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	2 years		...	984	126
63	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	21 months	1	...	928	119	0	0
64	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	21 months		...	905	119	0	0
65	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	5 months		...	897	263
66	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	21 months		...	892	116
67	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	19 months		...	890	122	0	0
68	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	18 months		...	876	123
69	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	19 months		...	867	117	0	0
70	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	13 months		...	859	121	0	0
71	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	17 months		...	819	124
72	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	17 months		...	819	118
73	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	17 months	1	...	804	119
74	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	22 months			792	90
75	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	4 months		...	775	365
76	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	13 months	1	1	682	132	0	0
77	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	5 weeks		...	644	370	0	9
78	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	10 months		...	582	128
79	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.0.1	10 months	1	...	552	124	0	0
80	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	10 months	1	...	546	112	0	0
81	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	5 months		...	337	139	0	0
82	bio qtlHD	(...) pre		pre				247	22
83	bio stockholm	Parse stockholm sequence alignment format (...) new	Ben J. Woodcroft	0.0.1	today		...	36	36	3	7

*) gem downloads (total & last 90 days) from rubygems.org as of 2013-06-19
**) number of commits on GitHub (last 7 days & last 90 days)