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Items: 1 to 20 of 79

1.

LOX: inferring Level Of eXpression from diverse methods of census sequencing.

Zhang Z, López-Giráldez F, Townsend JP.

Bioinformatics. 2010 Aug 1;26(15):1918-9. doi: 10.1093/bioinformatics/btq303. Epub 2010 Jun 10.

2.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

3.

The filamentous fungal gene expression database (FFGED).

Zhang Z, Townsend JP.

Fungal Genet Biol. 2010 Mar;47(3):199-204. doi: 10.1016/j.fgb.2009.12.001. Epub 2009 Dec 16.

4.

metahdep: meta-analysis of hierarchically dependent gene expression studies.

Stevens JR, Nicholas G.

Bioinformatics. 2009 Oct 1;25(19):2619-20. doi: 10.1093/bioinformatics/btp468. Epub 2009 Jul 30.

PMID:
19648140
5.

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
6.

SpeCond: a method to detect condition-specific gene expression.

Cavalli FM, Bourgon R, Vaquerizas JM, Luscombe NM.

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101. Erratum in: Genome Biol. 2011;12(12):413. Huber, Wolfgang [removed].

7.

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data.

Ma S, Jiang T, Jiang R.

Bioinformatics. 2015 Feb 15;31(4):563-71. doi: 10.1093/bioinformatics/btu672. Epub 2014 Oct 15.

PMID:
25322838
8.

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.

Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF.

Bioinformatics. 2010 Nov 1;26(21):2792-3. doi: 10.1093/bioinformatics/btq503. Epub 2010 Sep 1.

9.

ArrayD: a general purpose software for microarray design.

Sharma A, Srivastava GP, Sharma VK, Ramachandran S.

BMC Bioinformatics. 2004 Oct 2;5:142.

10.

SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy.

Gatti DM, Sypa M, Rusyn I, Wright FA, Barry WT.

Bioinformatics. 2009 Feb 15;25(4):541-2. doi: 10.1093/bioinformatics/btn655. Epub 2008 Dec 19.

11.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.

Wang L, Feng Z, Wang X, Wang X, Zhang X.

Bioinformatics. 2010 Jan 1;26(1):136-8. doi: 10.1093/bioinformatics/btp612. Epub 2009 Oct 24.

PMID:
19855105
12.

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.

Conde L, Montaner D, Burguet-Castell J, Tárraga J, Medina I, Al-Shahrour F, Dopazo J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W81-5. Epub 2007 Apr 27.

13.

Analyzing microarray data using WebArray.

Wang Y, McClelland M, Xia XQ.

Cold Spring Harb Protoc. 2009 Aug;2009(8):pdb.prot5260. doi: 10.1101/pdb.prot5260. No abstract available.

PMID:
20147236
14.

SVS: data and knowledge integration in computational biology.

Zycinski G, Barla A, Verri A.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:6474-8. doi: 10.1109/IEMBS.2011.6091598.

PMID:
22255821
15.

Bayesian model-based clustering of temporal gene expression using autoregressive panel data approach.

Nascimento M, Sáfadi T, Fonseca e Silva F, Nascimento AC.

Bioinformatics. 2012 Aug 1;28(15):2004-7. doi: 10.1093/bioinformatics/bts322. Epub 2012 Jun 4.

PMID:
22668790
16.

Software and methods for oligonucleotide and cDNA array data analysis.

Zapala MA, Lockhart DJ, Pankratz DG, Garcia AJ, Barlow C, Lockhart DJ.

Genome Biol. 2002;3(6):SOFTWARE0001. Epub 2002 May 23.

17.

A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.

Beal MJ, Falciani F, Ghahramani Z, Rangel C, Wild DL.

Bioinformatics. 2005 Feb 1;21(3):349-56. Epub 2004 Sep 7.

PMID:
15353451
18.

Smoothing waves in array CGH tumor profiles.

van de Wiel MA, Brosens R, Eilers PH, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B.

Bioinformatics. 2009 May 1;25(9):1099-104. doi: 10.1093/bioinformatics/btp132. Epub 2009 Mar 10.

PMID:
19276148
19.

The use of open source bioinformatics tools to dissect transcriptomic data.

Nitsche BM, Ram AF, Meyer V.

Methods Mol Biol. 2012;835:311-31. doi: 10.1007/978-1-61779-501-5_19.

PMID:
22183662
20.

Cross-hybridization modeling on Affymetrix exon arrays.

Kapur K, Jiang H, Xing Y, Wong WH.

Bioinformatics. 2008 Dec 15;24(24):2887-93. doi: 10.1093/bioinformatics/btn571. Epub 2008 Nov 4.

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