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	2 days	30	14	40684	4134	8	82
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.0.1	2 weeks		...	20742	1970	0	37
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.4	13 months	14	11	18171	1847	0	18
4	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	0.6.0	5 months		...	14055	1545	0	0
5	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	21 months	4	...	12047	1204	0	0
6	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.5.2	5 months		...	10374	1126	0	24
7	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	9 months	6	2	9662	908	0	0
8	intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis	1.01.00	2 months			9637	1108
9	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.5	4 weeks		...	8086	1190	0	16
10	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	13 months	4	2	7407	550	0	0
11	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	9 months		...	6530	1145
12	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	3 months	10	...	5247	564	0	1
13	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	7 months		...	5121	1044	0	0
14	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	11 months		...	4873	642
15	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	17 months		...	4871	437
16	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.6	3 weeks		...	4787	2206	0	10
17	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.7	11 months	5	4	4635	564	0	1
18	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	2 years	4	...	4395	372	0	0
19	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	3 years			4382	306
20	scaffolder	Genome scaffolding for human beings (...)	Michael Barton	0.4.4	21 months		...	4320	375
21	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	3 months		...	4126	556
22	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	5 years			4086	284
23	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	12 months	6	1	3998	355	0	0
24	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.5	3 weeks		...	3860	470	0	21
25	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.0	2 years		...	3767	318	0	0
26	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	15 months	3	...	3720	374	0	0
27	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	2 years		...	3563	320	0	0
28	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	9 months		...	3513	439	0	0
29	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	2 years		...	3474	277	0	0
30	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	0.8.0	6 months		...	3418	620	0	3
31	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	5 months	2	...	3394	435	0	0
32	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	11 months		...	3386	306	0	11
33	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	2 years		...	3176	230
34	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.3.2	6 weeks		...	3090	1137	0	19
35	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	9 months		...	3070	457	0	0
36	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	2 years		...	2996	215	0	0
37	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	2 years		...	2714	269	0	0
38	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	24 months	1	...	2585	268	0	0
39	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	6 months	1	...	2352	284	0	0
40	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	2 years		...	2262	199	0	0
41	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	16 months		...	2236	182	0	0
42	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.1	8 weeks	5	...	2208	507	0	3
43	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	9 months		...	2087	367	0	0
44	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	12 months		1	1898	187	0	0
45	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	17 months		...	1833	206
46	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	21 months		...	1730	172	0	0
47	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	12 months		...	1581	185
48	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	9 months			1562	279
49	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	16 months	1	...	1523	165	0	0
50	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	10 months	1	1	1521	251	0	0
51	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	0.2.2	2 weeks		...	1456	606	0	41
52	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	5 months	1	...	1454	294	0	0
53	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	4 weeks		...	1432	396	0	28
54	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	7 months		...	1420	281	0	0
55	bio tabix	Ruby binding for samtools tabix (...)	throwern	0.1.3	12 months	3	...	1251	184	0	0
56	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	12 months		...	1194	184	0	0
57	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	20 months		1	1182	90	0	0
58	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	3 years			1175	85
59	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	2 years		...	1166	108	0	0
60	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	2 years		...	1157	107	0	0
61	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	6 months	3	...	1012	191	0	0
62	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	2 years		...	946	104	0	0
63	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	21 months		...	892	98
64	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	20 months		...	869	94	0	0
65	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	20 months		...	854	94	0	0
66	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	19 months		...	848	94	0	0
67	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	17 months	3	...	837	99	0	0
68	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	19 months	2	...	828	95	0	0
69	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	12 months		...	821	96	0	0
70	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	5 months	1	...	810	208	0	0
71	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	16 months	1	...	783	97	0	0
72	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	16 months	1	...	779	96	0	0
73	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	16 months	1	...	768	98	0	0
74	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	22 months			763	75
75	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	3 months		...	673	331
76	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	12 months		...	644	108	0	0
77	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	9 months		...	543	104
78	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.0.1	9 months	1	...	514	101	0	0
79	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	9 months		...	509	89	0	0
80	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	1 week		...	506	246
81	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	4 months		...	296	117	0	0
82	bio qtlHD	(...) pre		pre				243	20

*) gem downloads (total & last 90 days) from rubygems.org as of 2013-05-26
**) number of commits on GitHub (last 7 days & last 90 days)