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GSVA: gene set variation analysis for microarray and RNA-Seq data
Article
Article
GSVA: gene set variation analysis for microarray and RNA-Seq data
Sonja Hänzelmann; Robert Castelo; Justin Guinney · BMC Bioinformatics · 2013
BACKGROUND: Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis...
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WGCNA: an R package for weighted correlation network analysis
Article
Article
WGCNA: an R package for weighted correlation network analysis
Peter Langfelder; Steve Horvath · BMC Bioinformatics · 2008
BACKGROUND: Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns a...
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An automated method for finding molecular complexes in large protein interaction networks
Article
Article
An automated method for finding molecular complexes in large protein interaction networks
Gary D. Bader; Christopher W.V. Hogue · BMC Bioinformatics · 2003
BACKGROUND: Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have a...
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MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Article
Article
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
R. C. Edgar · BMC Bioinformatics · 2004
BACKGROUND: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reporte...
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Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Article
Article
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Edward Y. Chen; Christopher M. Tan; Yan Kou; Qiaonan Duan; Zichen Wang; Gabriela Vaz Meirelles; Neil R. Clark; Avi Ma’ayan · BMC Bioinformatics · 2013
BACKGROUND: System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new ...
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