New: CloudBioLinux packages are now listed on biogems.info !
| # | biogem | description | by | cite | version | released | stars | issues | source | build | total | 90d*) | 7d | 90d**) | ||
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| downloads | commits | |||||||||||||||
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Bioinformatics library
(...)
|
BioRuby project |
2 days
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40684
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4134
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Parser of scientific names
(...)
|
Dmitry Mozzherin |
|
2 weeks
|
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20742
|
1970
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|
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Biogem is a software generator for Ruby in
(...)
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Raoul J.P. Bonnal, Pjotr Prins |
13 months
|
18171
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1847
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|||||||||||
|
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Binder of samtools for Ruby, on the top
(...)
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Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal |
|
5 months
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|
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14055
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1545
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||||||||
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Http requests to entrez e-utilities
(...)
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Jared Ning |
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21 months
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12047
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1204
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||||||||||
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The Ruby ucsc api: accessing the ucsc genome
(...)
|
Hiroyuki Mishima, Jan Aerts |
|
5 months
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10374
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1126
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||||||||
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Gff3 parser for big data
(...)
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Pjotr Prins |
9 months
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9662
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908
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|||||||||||
|
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Webservice client library for intermine data-warehouses
(...)
|
Alex Kalderimis |
|
2 months
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9637
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1108
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Blast search made easy!
(...)
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Anurag Priyam, Ben J Woodcroft, Yannick Wurm |
|
4 weeks
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|
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8086
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1190
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||||||||
|
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Log4r wrapper with extra features for roles and
(...)
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Pjotr Prins |
|
13 months
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7407
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550
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||||||||||
|
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Maf parser for BioRuby
(...)
|
Clayton Wheeler |
|
9 months
|
|
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6530
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1145
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||||||||
|
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Very fast blast xml parser and library for
(...)
|
Pjotr Prins |
3 months
|
5247
|
564
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|||||||||||
|
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A biogem to submit jobs on a queue
(...)
|
Francesco Strozzi |
|
7 months
|
|
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5121
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1044
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||||||||
|
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A fast parser for fastq files
(...)
|
Francesco Strozzi |
|
11 months
|
|
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4873
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642
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Pipeline to remove contaminations from est libraries
(...)
|
Philipp Comans |
|
17 months
|
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4871
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437
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||||||||
|
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Gadgets for bioinformatics
(...)
|
Shintaro Katayama |
|
3 weeks
|
|
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4787
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2206
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||||||||
|
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Support for multiple sequence alignments (msa)
(...)
|
Pjotr Prins |
|
11 months
|
4635
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564
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||||||||||
|
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BioRuby assembly plugin
(...)
|
Chase Miller, Francesco Strozzi |
|
2 years
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4395
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372
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||||||||||
|
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This is a development release
(...)
|
Pjotr Prins and Trevor Wennblom |
3 years
|
|
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4382
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306
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Genome scaffolding for human beings
(...)
|
Michael Barton |
21 months
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4320
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375
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A tool to classify and manipulate pfemp1 dbl-alpha
(...)
|
George Githinji |
|
3 months
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4126
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556
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||||||||
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Library for visualizing genomic regions
(...)
|
Jan Aerts |
|
5 years
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4086
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284
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BioRuby plugin for reading and writing nexml (http://nexml.org)
(...)
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Rutger Vos, Anurag Priyam |
|
12 months
|
3998
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355
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||||||||||
|
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Low memory sequence emitters
(...)
|
Pjotr Prins |
|
3 weeks
|
|
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3860
|
470
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||||||||
|
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Lightweight Ruby api for ncbi eutils
(...)
|
Joon Lee, aka seouri |
|
2 years
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|
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3767
|
318
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||||||||
|
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A BioRuby plugin for calculating the isoelectric point
(...)
|
George Githinji, Pascal Betz |
|
15 months
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3720
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374
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||||||||||
|
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A BioRuby plugin: handling genomic interavals and overlaps
(...)
|
Hiroyuki Mishima |
|
2 years
|
|
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3563
|
320
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||||||||
|
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A wrapper for the signal peptide prediction algorith
(...)
|
Ben J Woodcroft |
|
9 months
|
|
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3513
|
439
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||||||||
|
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Running and parsing of the protein transmembrane domain
(...)
|
Ben J Woodcroft |
|
2 years
|
|
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3474
|
277
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||||||||
|
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Swiss army knife of tabulated data; transforming/filtering tab/csv
(...)
|
Pjotr Prins |
|
6 months
|
|
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3418
|
620
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||||||||
|
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A BioRuby plugin for interaction with the transmembrane
(...)
|
Ben J. Woodcroft |
|
5 months
|
3394
|
435
|
||||||||||
|
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Bio-ngs provides a framework for handling ngs data
(...)
|
Francesco Strozzi, Raoul J.P. Bonnal |
|
11 months
|
|
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3386
|
306
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||||||||
|
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Gene ontology (go) interface for Ruby
(...)
|
Ben J Woodcroft |
|
2 years
|
|
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3176
|
230
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||||||||
|
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Create pretty svg-format images of features, gene models
(...)
|
Dan MacLean |
|
6 weeks
|
|
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3090
|
1137
|
||||||||
|
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Ruby wrapper for sambamba tool
(...)
|
Artem Tarasov |
|
9 months
|
|
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3070
|
457
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||||||||
|
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Api to ensembl databases
(...)
|
Jan Aerts, Francesco Strozzi |
2 years
|
|
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2996
|
215
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|||||||||
|
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Ruby binding for bwa mapping software
(...)
|
Francesco Strozzi |
|
2 years
|
|
|
2714
|
269
|
||||||||
|
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A plugin that allows you to parse large
(...)
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robsyme |
|
24 months
|
2585
|
268
|
||||||||||
|
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Iterate through a samtools pileup file
(...)
|
Ben J. Woodcroft |
|
6 months
|
2352
|
284
|
||||||||||
|
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Geneexpression illuminahumanannotation
(...)
|
Raoul J.P. Bonnal |
|
2 years
|
|
|
2262
|
199
|
||||||||
|
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Implementation of the plasmoap algorithm
(...)
|
Ben J Woodcroft |
|
16 months
|
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2236
|
182
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||||||||
|
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A biogem for counting small kmers for fingerprinting
(...)
|
Ben J Woodcroft |
|
8 weeks
|
2208
|
507
|
||||||||||
|
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Reading/writing bgzf blocks
(...)
|
Artem Tarasov, Clayton Wheeler |
|
9 months
|
|
|
2087
|
367
|
||||||||
|
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Bioinformatics triple-store support
(...)
|
Pjotr Prins |
|
12 months
|
|
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1898
|
187
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||||||||
|
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Parse affymetrix cel/cdf files
(...)
|
Pjotr Prins |
|
17 months
|
|
|
1833
|
206
|
||||||||
|
|
BioRuby core plugins, most and stable plugins. blastxmlparser,
(...)
|
Raoul J.P. Bonnal |
21 months
|
|
|
1730
|
172
|
|||||||||
|
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Programmatic interface to the cnls nuclear localisation signal
(...)
|
Ben J. Woodcroft |
|
12 months
|
|
|
1581
|
185
|
||||||||
|
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Ruby wrapper for the gff3-pltools
(...)
|
Marjan Povolni |
|
9 months
|
|
|
1562
|
279
|
||||||||
|
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Enables the localisation predictor wolf psort to be
(...)
|
Ben J Woodcroft |
|
16 months
|
1523
|
165
|
||||||||||
|
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Chembl rest api client, parser and container
(...)
|
Mitsuteru Nakao |
|
10 months
|
1521
|
251
|
||||||||||
|
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An open source framework for transforming heterogeneous data
(...)
|
Joachim Baran, Kevin B. Cohen, Geraint Duck et al. |
|
2 weeks
|
|
|
1456
|
606
|
||||||||
|
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Next-generation mapping of mutations
(...)
|
Dan MacLean |
|
5 months
|
1454
|
294
|
||||||||||
|
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Read and manipulate cd-hit clusters
(...)
|
George Githinji |
|
4 weeks
|
|
|
1432
|
396
|
||||||||
|
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Ruby binding to the ucsc kent utilities
(...)
|
throwern |
|
7 months
|
|
|
1420
|
281
|
||||||||
|
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Ruby binding for samtools tabix
(...)
|
throwern |
|
12 months
|
1251
|
184
|
||||||||||
|
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Parse pfam hmm definition files
(...)
|
Ben J. Woodcroft |
|
12 months
|
|
|
1194
|
184
|
||||||||
|
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Digests dna based on restriction enzyme cut patterns
(...)
|
Trevor Wennblom |
20 months
|
|
|
1182
|
90
|
|||||||||
|
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Does high pairwise alignment of sequencing reads with
(...)
|
John T. Prince |
|
3 years
|
|
|
1175
|
85
|
||||||||
|
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BioRuby plugin for sun grid engine
(...)
|
Toshiaki Katayama |
|
2 years
|
|
|
1166
|
108
|
||||||||
|
|
Hello world plugin for the BioRuby (just for
(...)
|
Toshiaki Katayama |
|
2 years
|
|
|
1157
|
107
|
||||||||
|
|
Bio-gag is a biogem for detecting and correcting
(...)
|
Ben J Woodcroft |
|
6 months
|
1012
|
191
|
||||||||||
|
|
A method to get the nucleotide sequence of
(...)
|
Ben J Woodcroft |
|
2 years
|
|
|
946
|
104
|
||||||||
|
|
BioRuby core ext: plugins which require external library
(...)
|
Raoul J.P. Bonnal, Pjotr Prins |
21 months
|
|
|
892
|
98
|
|||||||||
|
|
Restriction enzyme dataset
(...)
|
Sir Richard J. Roberts, Trevor Wennblom |
|
20 months
|
|
|
869
|
94
|
||||||||
|
|
Meta package for biolinux distribution
(...)
|
Raoul J.P. Bonnal |
|
20 months
|
|
|
854
|
94
|
||||||||
|
|
One-line summary of your gem
(...)
|
Toshiaki Katayama |
|
19 months
|
|
|
848
|
94
|
||||||||
|
|
A Ruby api to the ensembl database
(...)
|
Jan Aerts, Francesco Strozzi |
17 months
|
837
|
99
|
|||||||||||
|
|
Decoding the dbsnp bitfield
(...)
|
Hiroyuki Mishima |
|
19 months
|
828
|
95
|
||||||||||
|
|
Phyloxml plugin for BioRuby
(...)
|
Diana Jaunzeikare, Clayton Wheeler |
|
12 months
|
|
|
821
|
96
|
||||||||
|
|
A protparam compatible utility for BioRuby
(...)
|
hryk |
|
5 months
|
810
|
208
|
||||||||||
|
|
A simple biogem that allows computation of the
(...)
|
Ben J Woodcroft |
|
16 months
|
783
|
97
|
||||||||||
|
|
Wrapper around the exportpred algorithm for predicting p
(...)
|
Ben J Woodcroft |
|
16 months
|
779
|
96
|
||||||||||
|
|
Hydropathy scale for BioRuby
(...)
|
Ben J Woodcroft |
|
16 months
|
768
|
98
|
||||||||||
|
|
Biological extensions for the intermine webservice client library
(...)
|
Alex Kalderimis |
|
22 months
|
|
|
|
763
|
75
|
|
|
|||||
|
|
BioRuby plugin for unichem rest web service
(...)
|
Mitsuteru Nakao |
|
3 months
|
|
|
673
|
331
|
||||||||
|
|
Enables parsing of hmmer version 3 reports
(...)
|
Christian Zmasek, Ben J Woodcroft |
|
12 months
|
|
|
644
|
108
|
||||||||
|
|
Build graph with jRuby
(...)
|
Matteo Picciolini |
|
9 months
|
|
|
543
|
104
|
||||||||
|
|
This biogem is built around krona, a flashy
(...)
|
Ben J. Woodcroft |
|
9 months
|
514
|
101
|
||||||||||
|
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A programmatic interface to the ipcress in-silico pcr
(...)
|
Ben J Woodcroft |
|
9 months
|
|
|
509
|
89
|
||||||||
|
|
Reports whether a nucleotide change results in synonymous
(...)
|
Dan MacLean |
|
1 week
|
|
|
506
|
246
|
||||||||
|
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Reads metadata from integrated microbial genomes (img) metadata
(...)
|
Ben J. Woodcroft |
|
4 months
|
|
|
296
|
117
|
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(...)
pre
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243
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20
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*) 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)
**) number of commits on GitHub (last 7 days & last 90 days)