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Authors: John Quackenbush
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Journal Article

Higher-order correction of persistent batch effects in correlation networks Open Access

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Soel Micheletti and others
Bioinformatics, Volume 40, Issue 9, September 2024, btae531, https://doi.org/10.1093/bioinformatics/btae531
Published: 03 September 2024
Journal Article

PUMA: PANDA Using MicroRNA Associations Open Access

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Marieke L Kuijjer and others
Bioinformatics, Volume 36, Issue 18, September 2020, Pages 4765–4773, https://doi.org/10.1093/bioinformatics/btaa571
Published: 17 June 2020
Journal Article

Identification of differentially expressed gene sets using the Generalized Berk–Jones statistic Free

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Sheila M Gaynor and others
Bioinformatics, Volume 35, Issue 22, November 2019, Pages 4568–4576, https://doi.org/10.1093/bioinformatics/btz277
Published: 07 May 2019
Journal Article

Estimating gene regulatory networks with pandaR Open Access

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Daniel Schlauch and others
Bioinformatics, Volume 33, Issue 14, July 2017, Pages 2232–2234, https://doi.org/10.1093/bioinformatics/btx139
Published: 11 March 2017
Journal Article

BatchQC: interactive software for evaluating sample and batch effects in genomic data Open Access

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Solaiappan Manimaran and others
Bioinformatics, Volume 32, Issue 24, december 2016, Pages 3836–3838, https://doi.org/10.1093/bioinformatics/btw538
Published: 18 August 2016
Journal Article

PyPanda: a Python package for gene regulatory network reconstruction Open Access

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David G.P. van IJzendoorn and others
Bioinformatics, Volume 32, Issue 21, November 2016, Pages 3363–3365, https://doi.org/10.1093/bioinformatics/btw422
Published: 10 July 2016
Journal Article

RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface Free

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Markus S. Schröder and others
Bioinformatics, Volume 29, Issue 5, March 2013, Pages 666–668, https://doi.org/10.1093/bioinformatics/bts708
Published: 06 January 2013
Journal Article

iBBiG: iterative binary bi-clustering of gene sets Open Access

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Daniel Gusenleitner and others
Bioinformatics, Volume 28, Issue 19, October 2012, Pages 2484–2492, https://doi.org/10.1093/bioinformatics/bts438
Published: 12 July 2012
Journal Article

nEASE: a method for gene ontology subclassification of high-throughput gene expression data Free

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Thomas W. Chittenden and others
Bioinformatics, Volume 28, Issue 5, March 2012, Pages 726–728, https://doi.org/10.1093/bioinformatics/bts011
Published: 13 January 2012
Journal Article

RNA-Seq analysis in MeV Open Access

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Eleanor A. Howe and others
Bioinformatics, Volume 27, Issue 22, November 2011, Pages 3209–3210, https://doi.org/10.1093/bioinformatics/btr490
Published: 05 October 2011
Journal Article

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models Free

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Markus S. Schröder and others
Bioinformatics, Volume 27, Issue 22, November 2011, Pages 3206–3208, https://doi.org/10.1093/bioinformatics/btr511
Published: 07 September 2011
Journal Article

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV Free

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Jarupon Fah Sathirapongsasuti and others
Bioinformatics, Volume 27, Issue 19, October 2011, Pages 2648–2654, https://doi.org/10.1093/bioinformatics/btr462
Published: 09 August 2011
Journal Article

Defining an informativeness metric for clustering gene expression data Open Access

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Jessica C. Mar and others
Bioinformatics, Volume 27, Issue 8, April 2011, Pages 1094–1100, https://doi.org/10.1093/bioinformatics/btr074
Published: 16 February 2011
Journal Article

Papers on normalization, variable selection, classification or clustering of microarray data Free

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David M. Rocke and others
Bioinformatics, Volume 25, Issue 6, March 2009, Pages 701–702, https://doi.org/10.1093/bioinformatics/btp038
Published: 09 February 2009
Journal Article

Editorial Free

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Alex Bateman and John Quackenbush
Bioinformatics, Volume 25, Issue 4, February 2009, Page 429, https://doi.org/10.1093/bioinformatics/btp037
Published: 08 February 2009
Journal Article

Microarray blob-defect removal improves array analysis Free

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Jun S. Song and others
Bioinformatics, Volume 23, Issue 8, April 2007, Pages 966–971, https://doi.org/10.1093/bioinformatics/btm043
Published: 01 March 2007
Journal Article

It is time to end the patenting of software Free

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John Quackenbush and Steven L. Salzberg
Bioinformatics, Volume 22, Issue 12, June 2006, Pages 1416–1417, https://doi.org/10.1093/bioinformatics/btl167
Published: 15 June 2006
Journal Article

MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms Free

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Amira Djebbari and others
Bioinformatics, Volume 21, Issue 15, August 2005, Pages 3324–3326, https://doi.org/10.1093/bioinformatics/bti503
Published: 26 May 2005
Journal Article

CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data Free

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Adam A. Margolin and others
Bioinformatics, Volume 21, Issue 15, August 2005, Pages 3308–3311, https://doi.org/10.1093/bioinformatics/bti500
Published: 19 May 2005
Journal Article

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets Free

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Geo Pertea and others
Bioinformatics, Volume 19, Issue 5, March 2003, Pages 651–652, https://doi.org/10.1093/bioinformatics/btg034
Published: 22 March 2003