Package: SEtools 1.19.0

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_1.19.0.tar.gz
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SEtools.pdf |SEtools.html✨
SEtools/json (API)
NEWS

# 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-1.19.0(bioc 3.20)SEtools-1.18.0(bioc 3.19)

bioconductor-package

9 exports 0.61 score 118 dependencies

Last updated 2 months agofrom:dc6b961626

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 fansi farver fastmap foreach formatR futile.logger futile.options gclus genefilter GenomeInfoDb GenomeInfoDbData 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 munsell nlme openssl openxlsx permute pheatmap pillar pkgconfig plogr png qap R6 randomcoloR RColorBrewer Rcpp RcppArmadillo registry rjson rlang RSQLite Rtsne S4Arrays S4Vectors scales sechm seriation shape snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys tibble TSP UCSC.utils utf8 V8 vctrs vegan viridisLite withr XML xtable XVector zip zlibbioc

SEtools

Pierre-Luc Germain

Rendered fromSEtools.Rmdusingknitr::rmarkdownon Jun 30 2024.

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