TSEA Manual

User Manual:

Open the PDF directly: View PDF PDF .
Page Count: 12

Scroll down to view the document on your mobile browser.

Ad

TSEA-package
tsea.analysis
tsea.analysis.multiple
tsea.expression.decode
tsea.expression.normalization
tsea.plot
tsea.summary
Index

Package ‘TSEA’August 21, 2018Type PackageTitle Tissue-Speciﬁc Enrichment AnalysisVersion 1.0Date 2018-08-21Author Guangsheng PeiMaintainer Guangsheng Pei <peiguangsheng@gmail.com>Imports pheatmap, RColorBrewerDescription Tissue-speciﬁc enrichment analysis to assess lists of candidate genes or RNA-Seq expression proﬁles.License GPL (>= 2)NeedsCompilation noRtopics documented:TSEA-package ....................................... 1tsea.analysis......................................... 4tsea.analysis.multiple.................................... 6tsea.expression.decode ................................... 7tsea.expression.normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8tsea.plot........................................... 9tsea.summary ........................................ 10Index 12TSEA-package Tissue-Speciﬁc Enrichment Analysis Tissue-Speciﬁc Enrichment Anal-ysisDescriptionTissue-speciﬁc enrichment analysis to assess lists of candidate genes and tissue-speciﬁc expressiondecode analysis for RNA-seq data to decode RNA expression matrices tissue heterogeneity.1

2TSEA-packageDetailsSince disease and physiological condition are often associated with a speciﬁc tissue, understandingthe tissue-speciﬁc genes (TSG) expression patterns will substantially reduce false discoveries inbiomedical research. However, due to cell complexity in human system, heterogeneous tissues arefrequently collected. Making it difﬁcult to distinguish gene expression variability and mislead resultinterpretation. Here, we present TSEA, an R package that conducts Tissue-Speciﬁc EnrichmentAnalysis (TSEA) using two built-in reference panels: the Genotype-Tissue Expression (GTEx) dataand the ENCyclopedia Of DNA Elements (ENCODE) data. We implemented two major functionsin TSEA to assess lists of candidate genes or expression matrices.The DESCRIPTION ﬁle:Package: TSEAType: PackageTitle: Tissue-Speciﬁc Enrichment AnalysisVersion: 1.0Date: 2018-08-21Author: Guangsheng PeiMaintainer: Guangsheng Pei <peiguangsheng@gmail.com>Imports: pheatmap, RColorBrewerDescription: Tissue-speciﬁc enrichment analysis to assess lists of candidate genes or RNA-Seq expression proﬁles.License: GPL (>= 2)Index of help topics:TSEA-package Tissue-Specific Enrichment AnalysisTissue-Specific Enrichment Analysistsea.analysis Tissue-specific enrichment analysis for querygene listtsea.analysis.multipleTissue-specific enrichment analysis for multiquery gene liststsea.expression.decodeTissue-specific enrichment analysis for RNA-Seqexpression profilestsea.expression.normalizationRNA-Seq expression profiles normalizationtsea.plot Tissue-specific enrichment analysis resultheatmap plottsea.summary Tissue-specific enrichment analysis resultsummaryAuthor(s)Guangsheng PeiMaintainer: Guangsheng PeiReferencesPei G., Dai Y., Zhao Z. Jia P. (2018) Tissue-Speciﬁc Enrichment Analysis (TSEA) to decode tissueheterogeneity. Bioinformatics, In submission.

Navigation menu