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]

# 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.

immunooncology experimentaldesign sequencing rnaseq geneexpression differentialexpression cpp

5.40 score 25 scripts 13 mentions 12 exports 201 dependencies

Last updated from:19363e32ea. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	242
linux-devel-arm64	NOTE	474
linux-devel-x86_64	NOTE	561
source / vignettes	OK	464
linux-release-arm64	NOTE	442
linux-release-x86_64	NOTE	541
macos-release-arm64	NOTE	470
macos-release-x86_64	NOTE	761
macos-oldrel-arm64	NOTE	290
macos-oldrel-x86_64	NOTE	600
windows-devel	NOTE	482
windows-release	NOTE	456
windows-oldrel	NOTE	407
wasm-release	OK	192

Exports:analyze_dataset convertIdOneToOne est_count_dispersion est_power est_power_curve est_power_distribution optimize_parameter plot_gene_counts_range plot_mappedReads_percent plot_power_curve sample_size sample_size_distribution

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob boot broom BSgenome bslib bumphunter cachem car carData checkmate cigarillo cli clipr cluster codetools colorspace corrplot cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray derfinder derfinderHelper Deriv digest doBy doRNG downloader dplyr edgeR evaluate farver fastcluster fastmap filelock fontawesome foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges GEOquery ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable heatmap3 highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma lme4 lmtest locfit magrittr MASS matlab Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plyr png polynom prettyunits progress purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr recount reformulas rentrez reshape2 restfulr Rhtslib rjson rlang rmarkdown RnaSeqSampleSizeData rngtools rpart Rsamtools RSQLite rstatix rstudioapi rtracklayer rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex tzdb UCSC.utils urca utf8 VariantAnnotation vctrs viridisLite vroom withr xfun XML xml2 XVector yaml zoo

RnaSeqSampleSize: Sample size estimation by real data

1 Introduction | 2 User friendly web interface | 3 Examples

Rendered fromRnaSeqSampleSize.Rnwusingknitr::knitr

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

Help page	Topics
analyze_dataset	analyze_dataset
convertId	convertIdOneToOne
est_count_dispersion	est_count_dispersion
est_power	est_power
est_power_curve	est_power_curve
est_power_distribution	est_power_distribution
optimize_parameter	optimize_parameter
plot_gene_counts_range	plot_gene_counts_range
plot_mappedReads_percent	plot_mappedReads_percent
plot_power_curve	plot_power_curve
sample_size	sample_size
sample_size_distribution	sample_size_distribution

Package: RnaSeqSampleSize 2.23.0

RnaSeqSampleSize: RnaSeqSampleSize

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Usage by other packages (reverse dependencies)