Package: RnaSeqSampleSize 2.23.0

Shilin Zhao Developer

RnaSeqSampleSize: RnaSeqSampleSize

RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data. It controls FDR for multiple testing and utilizes the average read count and dispersion distributions from real data to estimate a more reliable sample size. It is also equipped with several unique features, including estimation for interested genes or pathway, power curve visualization, and parameter optimization.

Authors:Shilin Zhao Developer [aut, cre], Chung-I Li [aut], Yan Guo [aut], Quanhu Sheng [aut], Yu Shyr [aut]

RnaSeqSampleSize_2.23.0.tar.gz
RnaSeqSampleSize_2.23.0.zip(r-4.7)RnaSeqSampleSize_2.23.0.zip(r-4.6)RnaSeqSampleSize_2.23.0.zip(r-4.5)
RnaSeqSampleSize_2.23.0.tgz(r-4.6-x86_64)RnaSeqSampleSize_2.23.0.tgz(r-4.6-arm64)RnaSeqSampleSize_2.23.0.tgz(r-4.5-x86_64)RnaSeqSampleSize_2.23.0.tgz(r-4.5-arm64)
RnaSeqSampleSize_2.23.0.tar.gz(r-4.7-arm64)RnaSeqSampleSize_2.23.0.tar.gz(r-4.7-x86_64)RnaSeqSampleSize_2.23.0.tar.gz(r-4.6-arm64)RnaSeqSampleSize_2.23.0.tar.gz(r-4.6-x86_64)
RnaSeqSampleSize_2.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RnaSeqSampleSize/json (API)
NEWS

# Install 'RnaSeqSampleSize' in R:
install.packages('RnaSeqSampleSize', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:RnaSeqSampleSize-2.23.0(bioc 3.24)RnaSeqSampleSize-2.22.0(bioc 3.23)

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

immunooncologyexperimentaldesignsequencingrnaseqgeneexpressiondifferentialexpressioncpp

5.40 score 25 scripts 400 downloads 13 mentions 12 exports 201 dependencies

Last updated from:19363e32ea. Checks:1 WARNING, 9 NOTE, 2 OK, 2 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING241
linux-devel-arm64NOTE415
linux-devel-x86_64NOTE651
source / vignettesOK407
linux-release-arm64NOTE422
linux-release-x86_64NOTE521
macos-release-arm64NOTE335
macos-release-x86_64ERROR536
macos-oldrel-arm64NOTE270
macos-oldrel-x86_64ERROR723
windows-develNOTE441
windows-releaseNOTE466
windows-oldrelNOTE469
wasm-releaseOK203

Exports:analyze_datasetconvertIdOneToOneest_count_dispersionest_powerest_power_curveest_power_distributionoptimize_parameterplot_gene_counts_rangeplot_mappedReads_percentplot_power_curvesample_sizesample_size_distribution

Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbroomBSgenomebslibbumphuntercachemcarcarDatacheckmatecigarilloclicliprclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayderfinderderfinderHelperDerivdigestdoBydoRNGdownloaderdplyredgeRevaluatefarverfastclusterfastmapfilelockfontawesomeforeachforecastforeignformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesGEOqueryggplot2ggpubrggrepelggsciggsignifgluegridExtragtableheatmap3highrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalme4lmtestlocfitmagrittrMASSmatlabMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogresspurrrquantregqvalueR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrrecountreformulasrentrezreshape2restfulrRhtslibrjsonrlangrmarkdownRnaSeqSampleSizeDatarngtoolsrpartRsamtoolsRSQLiterstatixrstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfosnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetinytextzdbUCSC.utilsurcautf8VariantAnnotationvctrsviridisLitevroomwithrxfunXMLxml2XVectoryamlzoo

RnaSeqSampleSize: Sample size estimation by real data

Rendered fromRnaSeqSampleSize.Rnwusingknitr::knitron May 30 2026.

Last update: 2022-02-09
Started: 2014-12-13

Readme and manuals

Help Manual

Help pageTopics
analyze_datasetanalyze_dataset
convertIdconvertIdOneToOne
est_count_dispersionest_count_dispersion
est_powerest_power
est_power_curveest_power_curve
est_power_distributionest_power_distribution
optimize_parameteroptimize_parameter
plot_gene_counts_rangeplot_gene_counts_range
plot_mappedReads_percentplot_mappedReads_percent
plot_power_curveplot_power_curve
sample_sizesample_size
sample_size_distributionsample_size_distribution