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Items: 1 to 20 of 262

1.

PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches.

Watson-Haigh NS, Kadarmideen HN, Reverter A.

Bioinformatics. 2010 Feb 1;26(3):411-3. doi: 10.1093/bioinformatics/btp674. Epub 2009 Dec 9.

PMID:
20007253
2.

penalizedSVM: a R-package for feature selection SVM classification.

Becker N, Werft W, Toedt G, Lichter P, Benner A.

Bioinformatics. 2009 Jul 1;25(13):1711-2. doi: 10.1093/bioinformatics/btp286. Epub 2009 Apr 27.

PMID:
19398451
3.

Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.

Albanese D, Filosi M, Visintainer R, Riccadonna S, Jurman G, Furlanello C.

Bioinformatics. 2013 Feb 1;29(3):407-8. doi: 10.1093/bioinformatics/bts707. Epub 2012 Dec 14.

PMID:
23242262
4.

SIMoNe: Statistical Inference for MOdular NEtworks.

Chiquet J, Smith A, Grasseau G, Matias C, Ambroise C.

Bioinformatics. 2009 Feb 1;25(3):417-8. doi: 10.1093/bioinformatics/btn637. Epub 2008 Dec 10.

PMID:
19073589
5.

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks.

Reverter A, Chan EK.

Bioinformatics. 2008 Nov 1;24(21):2491-7. doi: 10.1093/bioinformatics/btn482. Epub 2008 Sep 10.

PMID:
18784117
6.

parmigene--a parallel R package for mutual information estimation and gene network reconstruction.

Sales G, Romualdi C.

Bioinformatics. 2011 Jul 1;27(13):1876-7. doi: 10.1093/bioinformatics/btr274. Epub 2011 Apr 29.

PMID:
21531770
7.

Model-based boosting in high dimensions.

Hothorn T, Bühlmann P.

Bioinformatics. 2006 Nov 15;22(22):2828-9. Epub 2006 Aug 29.

PMID:
16940323
8.

Libaffy: software for processing Affymetrix GeneChip data.

Eschrich SA, Hoerter AM.

Bioinformatics. 2007 Jun 15;23(12):1562-4. Epub 2007 Apr 26.

PMID:
17463032
9.

WGCNA: an R package for weighted correlation network analysis.

Langfelder P, Horvath S.

BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559.

10.

NetBioV: an R package for visualizing large network data in biology and medicine.

Tripathi S, Dehmer M, Emmert-Streib F.

Bioinformatics. 2014 Oct;30(19):2834-6. doi: 10.1093/bioinformatics/btu384. Epub 2014 Jun 12.

PMID:
24928209
11.

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.

Müssel C, Hopfensitz M, Kestler HA.

Bioinformatics. 2010 May 15;26(10):1378-80. doi: 10.1093/bioinformatics/btq124. Epub 2010 Apr 7.

PMID:
20378558
12.

SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.

Debastiani VJ, Pillar VD.

Bioinformatics. 2012 Aug 1;28(15):2067-8. doi: 10.1093/bioinformatics/bts325. Epub 2012 Jun 4.

PMID:
22668789
13.

GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures.

Li F, Cao Y, Han L, Cui X, Xie D, Wang S, Bo X.

OMICS. 2013 Feb;17(2):116-8. doi: 10.1089/omi.2012.0087.

PMID:
23374109
14.

stringgaussnet: from differentially expressed genes to semantic and Gaussian networks generation.

Chaplais E, Garchon HJ.

Bioinformatics. 2015 Dec 1;31(23):3865-7. doi: 10.1093/bioinformatics/btv450. Epub 2015 Jul 30.

PMID:
26231430
15.

pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery.

Johannes M, Fröhlich H, Sültmann H, Beissbarth T.

Bioinformatics. 2011 May 15;27(10):1442-3. doi: 10.1093/bioinformatics/btr157. Epub 2011 Mar 30.

PMID:
21450711
16.

synbreed: a framework for the analysis of genomic prediction data using R.

Wimmer V, Albrecht T, Auinger HJ, Schön CC.

Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335. Epub 2012 Jun 10.

PMID:
22689388
17.

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics.

Sakellariou A, Spyrou G.

BMC Bioinformatics. 2015 Sep 15;16:291. doi: 10.1186/s12859-015-0719-5.

18.

Identifying differentially expressed subnetworks with MMG.

Noirel J, Sanguinetti G, Wright PC.

Bioinformatics. 2008 Dec 1;24(23):2792-3. doi: 10.1093/bioinformatics/btn499. Epub 2008 Sep 25.

PMID:
18819939
19.

pegas: an R package for population genetics with an integrated-modular approach.

Paradis E.

Bioinformatics. 2010 Feb 1;26(3):419-20. doi: 10.1093/bioinformatics/btp696. Epub 2010 Jan 14.

PMID:
20080509
20.

Cassis: detection of genomic rearrangement breakpoints.

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF.

Bioinformatics. 2010 Aug 1;26(15):1897-8. doi: 10.1093/bioinformatics/btq301. Epub 2010 Jun 23.

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