Package: metaseqR2 1.17.0

Panagiotis Moulos

metaseqR2: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Authors:Panagiotis Moulos [aut, cre]

metaseqR2_1.17.0.tar.gz
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metaseqR2.pdf |metaseqR2.html✨
metaseqR2/json (API)
NEWS

# Install 'metaseqR2' in R:

install.packages('metaseqR2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pmoulos/metaseqr2/issues

Datasets:

hg19pvalues - P-values from human RNA-Seq data with two conditions, four samples
libsizeListMm9 - Mouse RNA-Seq data with two conditions, four samples
mm9GeneCounts - Mouse RNA-Seq data with two conditions, four samples
sampleListMm9 - Mouse RNA-Seq data with two conditions, four samples

On BioConductor:metaseqR2-1.17.0(bioc 3.20)metaseqR2-1.16.0(bioc 3.19)

bioconductor-package

54 exports 1.16 score 227 dependencies 1 mentions

Last updated 2 months agofrom:03f3b0b5e0

Exports:buildAnnotationDatabase buildCustomAnnotation combineBonferroni combineHarmonic combineMaxp combineMinp combineSimes combineWeight createSignalTracks diagplotAvgFtd diagplotBoxplot diagplotCor diagplotDeHeatmap diagplotEdaseq diagplotFiltered diagplotFtd diagplotMds diagplotNoiseq diagplotPairs diagplotRoc diagplotVenn diagplotVolcano downsampleCounts estimateAufcWeights estimateSimParams getAnnotation getDefaults getInstalledAnnotations getWeights importCustomAnnotation loadAnnotation makeSimDataSd makeSimDataTcc metaseqr2 metaseqrPlot metaTest normalizeAbsseq normalizeDeseq normalizeDeseq2 normalizeDss normalizeEdaseq normalizeEdger normalizeNbpseq normalizeNoiseq read2count readTargets statAbsseq statDeseq statDeseq2 statDss statEdger statLimma statNbpseq statNoiseq

Dependencies:abind ABSSeq affy affyio annotate AnnotationDbi aroma.light askpass assertthat base64enc beachmat BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob bookdown bootstrap BSgenome bslib bsseq ca cachem callr caTools class cli cluster codetools colorspace corrplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir dendextend DESeq2 diagram digest dplyr DSS DT EDASeq edgeR egg evaluate fansi farver fastmap filelock FMStable fontawesome foreach formatR fs futile.logger futile.options future future.apply gclus genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 globals glue gplots gridExtra gtable gtools harmonicmeanp HDF5Array heatmaply highr hms htmltools htmlwidgets httpuv httr httr2 hwriter interp ipred IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice latticeExtra lava lazyeval lifecycle limma listenv locfit log4r magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell NBPSeq nlme nnet numDeriv openssl pander parallelly permute pillar pkgconfig plogr plotly plyr png preprocessCore prettyunits processx prodlim progress progressr promises ps purrr pwalign qap qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl registry reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rmdformats rmeta rpart Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales seriation shape ShortRead snow SparseArray sparseMatrixStats SQUAREM statmod stringi stringr SummarizedExperiment SuppDists survcomp survival survivalROC sys tibble tidyr tidyselect tinytex TSP txdbmaker UCSC.utils utf8 vctrs vegan VennDiagram viridis viridisLite vsn webshot withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

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Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build a local annotation database for metaseqR2	buildAnnotationDatabase
Import custom annotation to the metaseqR2 annotation database from GTF file	buildCustomAnnotation
Combine p-values with Bonferroni's method	combineBonferroni
Combine p-values using weights	combineHarmonic
Combine p-values using the maximum p-value	combineMaxp
Combine p-values using the minimum p-value	combineMinp
Combine p-values with Simes' method	combineSimes
Combine p-values using weights	combineWeight
Create bigWig signal tracks	createSignalTracks
Create average False (or True) Discovery curves	diagplotAvgFtd
Boxplots wrapper for the metaseqR2 package	diagplotBoxplot
Summarized correlation plots	diagplotCor
Diagnostic heatmap of differentially expressed genes	diagplotDeHeatmap
Diagnostic plots based on the EDASeq package	diagplotEdaseq
Diagnostic plot for filtered genes	diagplotFiltered
Create False (or True) Positive (or Negative) curves	diagplotFtd
Multi-Dimensinal Scale plots or RNA-Seq samples	diagplotMds
Diagnostic plots based on the NOISeq package	diagplotNoiseq
Massive X-Y, M-D correlation plots	diagplotPairs
Create basic ROC curves	diagplotRoc
Venn diagrams when performing meta-analysis	diagplotVenn
(Interactive) volcano plots of differentially expressed genes	diagplotVolcano
Downsample read counts	downsampleCounts
Estimate AUFC weights	estimateAufcWeights
Estimate negative binomial parameters from real data	estimateSimParams
Annotation downloader	getAnnotation
Default parameters for several metaseqr functions	getDefaults
Load a metaseqR2 annotation element	getInstalledAnnotations
Get precalculated statistical test weights	getWeights
p-values from human RNA-Seq data with two conditions, four samples	hg19pvalues
Import a metaseqR2 custom annotation element	importCustomAnnotation
Mouse RNA-Seq data with two conditions, four samples	libsizeListMm9
Load a metaseqR2 annotation element	loadAnnotation
Create simulated counts using the Soneson-Delorenzi method	makeSimDataSd
Create simulated counts using TCC package	makeSimDataTcc
The main metaseqr2 pipeline	metaseqr2
Diagnostic plots for the metaseqR2 package	metaseqrPlot
Meta-analysis using several RNA-Seq statistics	metaTest
Mouse RNA-Seq data with two conditions, four samples	mm9GeneCounts
Normalization based on the ABSSeq package	normalizeAbsseq
Normalization based on the DESeq package	normalizeDeseq
Normalization based on the DESeq2 package	normalizeDeseq2
Normalization based on the DSS package	normalizeDss
Normalization based on the EDASeq package	normalizeEdaseq
Normalization based on the edgeR package	normalizeEdger
Normalization based on the NBPSeq package	normalizeNbpseq
Normalization based on the NOISeq package	normalizeNoiseq
SAM/BAM/BED file reader helper for the metaseqr2 pipeline	read2count
Creates sample list and BAM/BED file list from file	readTargets
Mouse RNA-Seq data with two conditions, four samples	sampleListMm9
Statistical testing with ABSSeq	statAbsseq
Statistical testing with DESeq	statDeseq
Statistical testing with DESeq2	statDeseq2
Statistical testing with DSS	statDss
Statistical testing with edgeR	statEdger
Statistical testing with limma	statLimma
Statistical testing with NBPSeq	statNbpseq
Statistical testing with NOISeq	statNoiseq