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| # | 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 |
3 weeks
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42387
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5296
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Parser of scientific names
(...)
|
Dmitry Mozzherin |
|
1 day
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21637
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2573
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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 |
14 months
|
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18911
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2285
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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 |
|
6 months
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14663
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1907
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||||||||||
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Http requests to entrez e-utilities
(...)
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Jared Ning |
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22 months
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12576
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1484
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||||||||||
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The Ruby ucsc api: accessing the ucsc genome
(...)
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Hiroyuki Mishima, Jan Aerts |
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6 months
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10846
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1406
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||||||||
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Webservice client library for intermine data-warehouses
(...)
|
Alex Kalderimis |
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3 months
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10059
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1320
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Gff3 parser for big data
(...)
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Pjotr Prins |
10 months
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10022
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1118
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|||||||||
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Blast search made easy!
(...)
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Anurag Priyam, Ben J Woodcroft, Yannick Wurm |
|
7 weeks
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8555
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1432
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Log4r wrapper with extra features for roles and
(...)
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Pjotr Prins |
|
14 months
|
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7605
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659
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|
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Maf parser for BioRuby
(...)
|
Clayton Wheeler |
|
10 months
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6985
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1421
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||||||||||
|
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Gadgets for bioinformatics
(...)
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Shintaro Katayama |
|
1 week
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5718
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2829
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||||||||
|
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A biogem to submit jobs on a queue
(...)
|
Francesco Strozzi |
|
7 months
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5537
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1270
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||||||||
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Very fast blast xml parser and library for
(...)
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Pjotr Prins |
4 months
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5472
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686
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|||||||||||
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A fast parser for fastq files
(...)
|
Francesco Strozzi |
|
12 months
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5118
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786
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||||||||||
|
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Pipeline to remove contaminations from est libraries
(...)
|
Philipp Comans |
|
18 months
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5040
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533
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||||||||
|
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Support for multiple sequence alignments (msa)
(...)
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Pjotr Prins |
|
11 months
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4851
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689
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BioRuby assembly plugin
(...)
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Chase Miller, Francesco Strozzi |
|
2 years
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4538
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453
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||||||||
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This is a development release
(...)
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Pjotr Prins and Trevor Wennblom |
3 years
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4503
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378
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Genome scaffolding for human beings
(...)
|
Michael Barton |
22 months
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4462
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429
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A tool to classify and manipulate pfemp1 dbl-alpha
(...)
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George Githinji |
|
3 months
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4332
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666
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||||||||||
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Library for visualizing genomic regions
(...)
|
Jan Aerts |
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5 years
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4193
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345
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BioRuby plugin for reading and writing nexml (http://nexml.org)
(...)
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Rutger Vos, Anurag Priyam |
|
13 months
|
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4142
|
442
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||||||||
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Low memory sequence emitters
(...)
|
Pjotr Prins |
|
6 weeks
|
4043
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595
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||||||||||
|
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Lightweight Ruby api for ncbi eutils
(...)
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Joon Lee, aka seouri |
|
2 years
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3903
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389
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||||||||
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A BioRuby plugin for calculating the isoelectric point
(...)
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George Githinji, Pascal Betz |
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15 months
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3864
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461
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||||||||
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A wrapper for the signal peptide prediction algorith
(...)
|
Ben J Woodcroft |
|
10 months
|
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3690
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545
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||||||||
|
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A BioRuby plugin: handling genomic interavals and overlaps
(...)
|
Hiroyuki Mishima |
|
2 years
|
3685
|
395
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||||||||||
|
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Swiss army knife of tabulated data; transforming/filtering tab/csv
(...)
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Pjotr Prins |
|
7 months
|
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3663
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758
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||||||||
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Create pretty svg-format images of features, gene models
(...)
|
Dan MacLean |
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1 week
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3590
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1435
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||||||||||
|
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Running and parsing of the protein transmembrane domain
(...)
|
Ben J Woodcroft |
|
2 years
|
3582
|
338
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||||||||||
|
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A BioRuby plugin for interaction with the transmembrane
(...)
|
Ben J. Woodcroft |
|
6 months
|
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3570
|
535
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||||||||
|
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Bio-ngs provides a framework for handling ngs data
(...)
|
Francesco Strozzi, Raoul J.P. Bonnal |
|
12 months
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3490
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372
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||||||||
|
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Gene ontology (go) interface for Ruby
(...)
|
Ben J Woodcroft |
|
2 years
|
3266
|
279
|
||||||||||
|
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Ruby wrapper for sambamba tool
(...)
|
Artem Tarasov |
|
10 months
|
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3246
|
552
|
||||||||
|
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Api to ensembl databases
(...)
|
Jan Aerts, Francesco Strozzi |
2 years
|
3084
|
255
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|||||||||||
|
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Ruby binding for bwa mapping software
(...)
|
Francesco Strozzi |
|
2 years
|
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2824
|
342
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||||||||
|
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A plugin that allows you to parse large
(...)
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robsyme |
|
2 years
|
2696
|
338
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||||||||||
|
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A biogem for counting small kmers for fingerprinting
(...)
|
Ben J Woodcroft |
|
2 weeks
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2489
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724
|
||||||||
|
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Iterate through a samtools pileup file
(...)
|
Ben J. Woodcroft |
|
7 months
|
2461
|
349
|
||||||||||
|
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Geneexpression illuminahumanannotation
(...)
|
Raoul J.P. Bonnal |
|
2 years
|
2331
|
232
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||||||||||
|
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Implementation of the plasmoap algorithm
(...)
|
Ben J Woodcroft |
|
17 months
|
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2306
|
220
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||||||||
|
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Reading/writing bgzf blocks
(...)
|
Artem Tarasov, Clayton Wheeler |
|
10 months
|
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2236
|
454
|
||||||||
|
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Bioinformatics triple-store support
(...)
|
Pjotr Prins |
|
13 months
|
1979
|
239
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||||||||||
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Parse affymetrix cel/cdf files
(...)
|
Pjotr Prins |
|
18 months
|
1908
|
247
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||||||||||
|
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An open source framework for transforming heterogeneous data
(...)
|
Joachim Baran, Kevin B. Cohen, Geraint Duck et al. |
|
1 week
|
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1813
|
883
|
||||||||
|
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BioRuby core plugins, most and stable plugins. blastxmlparser,
(...)
|
Raoul J.P. Bonnal |
21 months
|
|
|
1801
|
217
|
|||||||||
|
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Ruby wrapper for the gff3-pltools
(...)
|
Marjan Povolni |
|
10 months
|
|
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1672
|
341
|
||||||||
|
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Programmatic interface to the cnls nuclear localisation signal
(...)
|
Ben J. Woodcroft |
|
13 months
|
|
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1653
|
224
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||||||||
|
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Chembl rest api client, parser and container
(...)
|
Mitsuteru Nakao |
|
11 months
|
|
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1632
|
318
|
||||||||
|
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Enables the localisation predictor wolf psort to be
(...)
|
Ben J Woodcroft |
|
17 months
|
1597
|
217
|
||||||||||
|
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Read and manipulate cd-hit clusters
(...)
|
George Githinji |
|
7 weeks
|
|
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1589
|
508
|
||||||||
|
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Next-generation mapping of mutations
(...)
|
Dan MacLean |
|
6 months
|
1563
|
357
|
||||||||||
|
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Ruby binding to the ucsc kent utilities
(...)
|
throwern |
|
8 months
|
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1534
|
352
|
||||||||
|
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Ruby binding for samtools tabix
(...)
|
throwern |
|
13 months
|
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1319
|
223
|
||||||||
|
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Parse pfam hmm definition files
(...)
|
Ben J. Woodcroft |
|
13 months
|
1274
|
231
|
||||||||||
|
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Digests dna based on restriction enzyme cut patterns
(...)
|
Trevor Wennblom |
21 months
|
|
|
1215
|
111
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|||||||||
|
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Does high pairwise alignment of sequencing reads with
(...)
|
John T. Prince |
|
3 years
|
|
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1208
|
101
|
||||||||
|
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BioRuby plugin for sun grid engine
(...)
|
Toshiaki Katayama |
|
2 years
|
1203
|
129
|
||||||||||
|
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Hello world plugin for the BioRuby (just for
(...)
|
Toshiaki Katayama |
|
2 years
|
|
|
1194
|
129
|
||||||||
|
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Bio-gag is a biogem for detecting and correcting
(...)
|
Ben J Woodcroft |
|
7 months
|
|
|
1078
|
230
|
||||||||
|
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A method to get the nucleotide sequence of
(...)
|
Ben J Woodcroft |
|
2 years
|
|
|
984
|
126
|
||||||||
|
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BioRuby core ext: plugins which require external library
(...)
|
Raoul J.P. Bonnal, Pjotr Prins |
21 months
|
928
|
119
|
|||||||||||
|
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Restriction enzyme dataset
(...)
|
Sir Richard J. Roberts, Trevor Wennblom |
|
21 months
|
|
|
905
|
119
|
||||||||
|
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A protparam compatible utility for BioRuby
(...)
|
hryk |
|
5 months
|
|
|
897
|
263
|
||||||||
|
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Meta package for biolinux distribution
(...)
|
Raoul J.P. Bonnal |
|
21 months
|
|
|
892
|
116
|
||||||||
|
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One-line summary of your gem
(...)
|
Toshiaki Katayama |
|
19 months
|
|
|
890
|
122
|
||||||||
|
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A Ruby api to the ensembl database
(...)
|
Jan Aerts, Francesco Strozzi |
18 months
|
|
|
876
|
123
|
|||||||||
|
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Decoding the dbsnp bitfield
(...)
|
Hiroyuki Mishima |
|
19 months
|
|
|
867
|
117
|
||||||||
|
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Phyloxml plugin for BioRuby
(...)
|
Diana Jaunzeikare, Clayton Wheeler |
|
13 months
|
|
|
859
|
121
|
||||||||
|
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Wrapper around the exportpred algorithm for predicting p
(...)
|
Ben J Woodcroft |
|
17 months
|
|
|
819
|
124
|
||||||||
|
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A simple biogem that allows computation of the
(...)
|
Ben J Woodcroft |
|
17 months
|
|
|
819
|
118
|
||||||||
|
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Hydropathy scale for BioRuby
(...)
|
Ben J Woodcroft |
|
17 months
|
804
|
119
|
||||||||||
|
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Biological extensions for the intermine webservice client library
(...)
|
Alex Kalderimis |
|
22 months
|
|
|
|
792
|
90
|
|
|
|||||
|
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BioRuby plugin for unichem rest web service
(...)
|
Mitsuteru Nakao |
|
4 months
|
|
|
775
|
365
|
||||||||
|
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Enables parsing of hmmer version 3 reports
(...)
|
Christian Zmasek, Ben J Woodcroft |
|
13 months
|
682
|
132
|
||||||||||
|
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Reports whether a nucleotide change results in synonymous
(...)
|
Dan MacLean |
|
5 weeks
|
|
|
644
|
370
|
||||||||
|
|
Build graph with jRuby
(...)
|
Matteo Picciolini |
|
10 months
|
|
|
582
|
128
|
||||||||
|
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This biogem is built around krona, a flashy
(...)
|
Ben J. Woodcroft |
|
10 months
|
552
|
124
|
||||||||||
|
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A programmatic interface to the ipcress in-silico pcr
(...)
|
Ben J Woodcroft |
|
10 months
|
546
|
112
|
||||||||||
|
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Reads metadata from integrated microbial genomes (img) metadata
(...)
|
Ben J. Woodcroft |
|
5 months
|
|
|
337
|
139
|
||||||||
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(...)
pre
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247
|
22
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||||||
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Parse stockholm sequence alignment format
(...)
new
|
Ben J. Woodcroft |
|
today
|
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36
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36
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*) 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)
**) number of commits on GitHub (last 7 days & last 90 days)