Package: SEtools 1.27.0

Pierre-Luc Germain

SEtools: SEtools: tools for working with SummarizedExperiment

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

Authors:Pierre-Luc Germain [cre, aut]

SEtools_1.27.0.tar.gz
SEtools_1.27.0.zip(r-4.7)SEtools_1.27.0.zip(r-4.6)SEtools_1.27.0.zip(r-4.5)
SEtools_1.27.0.tgz(r-4.6-any)SEtools_1.27.0.tgz(r-4.5-any)
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SEtools_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SEtools/json (API)

# Install 'SEtools' in R:

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

Bug tracker:https://github.com/plger/setools/issues

Datasets:

SE - Example dataset

On BioConductor:SEtools-1.27.0(bioc 3.24)SEtools-1.26.0(bioc 3.23)

geneexpression

6.26 score 3 stars 100 scripts 9 exports 111 dependencies

Last updated from:67898208e5. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	246
linux-devel-x86_64	NOTE	369
source / vignettes	OK	270
linux-release-x86_64	NOTE	338
macos-release-arm64	NOTE	265
macos-oldrel-arm64	NOTE	212
windows-devel	NOTE	258
windows-release	NOTE	264
windows-oldrel	NOTE	257
wasm-release	OK	197

Exports:aggSE castSE flattenPB log2FC mergeSEs resetAllSEtoolsOptions se2xls sehm svacor

Dependencies:abind annotate AnnotationDbi askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 blob ca cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DBI DelayedArray DESeq2 digest doParallel edgeR farver fastmap foreach formatR futile.logger futile.options gclus genefilter generics GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable httr IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime nlme openssl openxlsx permute pheatmap pkgconfig png qap R6 randomcoloR RColorBrewer Rcpp RcppArmadillo registry rjson rlang RSQLite Rtsne S4Arrays S4Vectors S7 scales sechm Seqinfo seriation shape snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys TSP V8 vctrs vegan viridisLite withr XML xtable XVector zip

SEtools

Rendered fromSEtools.Rmdusingknitr::rmarkdown

Last update: 2022-11-27
Started: 2019-06-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
aggSE	aggSE
castSE	castSE
Example dataset	data SE
flattenPB	flattenPB
log2FC	log2FC
mergeSEs	mergeSEs
resetAllSEtoolsOptions	resetAllSEtoolsOptions
se2xlsx	se2xls
sehm	sehm
svacor	svacor