Package: NormExpression 0.1.1

NormExpression: Normalize Gene Expression Data using Evaluated Methods

It provides a framework and a fast and simple way for researchers to evaluate methods (particularly some data-driven methods or their own methods) and then select a best one for data normalization in the gene expression analysis, based on the consistency of metrics and the consistency of datasets. Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Deshui Yu, Hua Wang, Gustavo Glusman, Max Robinson, Lin Liu, Jishou Ruan and Shan Gao (2018) <doi:10.1101/251140>.

Authors:Zhenfeng Wu , Shan Gao

NormExpression_0.1.1.tar.gz
NormExpression_0.1.1.zip(r-4.5)NormExpression_0.1.1.zip(r-4.4)NormExpression_0.1.1.zip(r-4.3)
NormExpression_0.1.1.tgz(r-4.4-any)NormExpression_0.1.1.tgz(r-4.3-any)
NormExpression_0.1.1.tar.gz(r-4.5-noble)NormExpression_0.1.1.tar.gz(r-4.4-noble)
NormExpression_0.1.1.tgz(r-4.4-emscripten)NormExpression_0.1.1.tgz(r-4.3-emscripten)
NormExpression.pdf |NormExpression.html
NormExpression/json (API)

# Install 'NormExpression' in R:
install.packages('NormExpression', repos = c('https://gaoshant.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.16 score 2 stars 36 scripts 256 downloads 2 mentions 30 exports 0 dependencies

Last updated 8 months agofrom:e77fe377ae. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winOKNov 16 2024
R-4.5-linuxOKNov 16 2024
R-4.4-winOKNov 16 2024
R-4.4-macOKNov 16 2024
R-4.3-winOKNov 16 2024
R-4.3-macOKNov 16 2024

Exports:calcFactorRLEcalcFactorUpperquartilecalcFactorWeightedchange_coloursCV2AUCVCestimateSizeFactorsForMatrixfilteredZerofindGenesgatherCorsgatherCors4MatricesgatherCVsgatherCVs4MatricesgatherFactorsgetAreagetAUCVCgetAUCVCsgetCorgetCorMediansgetCVgetFactorsgetNormMatrixgridAUCVCgridAUCVC4MatricesidentifyUbqidentifyUbqRepeatnonzeroRatio2AUCVCoptTUplotCorsplotCVsplotHC

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
bkRNA18bkRNA18
bkRNA18_factorsbkRNA18_factors
calcFactorRLEcalcFactorRLE
calcFactorUpperquartilecalcFactorUpperquartile
calcFactorWeightedcalcFactorWeighted
change_colourschange_colours
CV2AUCVCCV2AUCVC
estimateSizeFactorsForMatrixestimateSizeFactorsForMatrix
filteredZerofilteredZero
findGenesfindGenes
gatherCorsgatherCors
gatherCors4MatricesgatherCors4Matrices
gatherCVsgatherCVs
gatherCVs4MatricesgatherCVs4Matrices
gatherFactorsgatherFactors
getAreagetArea
getAUCVCgetAUCVC
getAUCVCsgetAUCVCs
getCorgetCor
getCorMediansgetCorMedians
getCVgetCV
getFactorsgetFactors
getNormMatrixgetNormMatrix
gridAUCVCgridAUCVC
gridAUCVC4MatricesgridAUCVC4Matrices
identifyUbqidentifyUbq
identifyUbqRepeatidentifyUbqRepeat
nonzeroRatio2AUCVCnonzeroRatio2AUCVC
optTUoptTU
plotCorsplotCors
plotCVsplotCVs
plotHCplotHC
scRNA663scRNA663
scRNA663_factorsscRNA663_factors