Package: sechm 1.21.0

Pierre-Luc Germain

sechm: sechm: Complex Heatmaps from a SummarizedExperiment

sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.

Authors:Pierre-Luc Germain [cre, aut]

sechm_1.21.0.tar.gz
sechm_1.21.0.zip(r-4.7)sechm_1.21.0.zip(r-4.6)sechm_1.21.0.zip(r-4.5)
sechm_1.21.0.tgz(r-4.6-any)sechm_1.21.0.tgz(r-4.5-any)
sechm_1.21.0.tar.gz(r-4.7-any)sechm_1.21.0.tar.gz(r-4.6-any)
sechm_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sechm/json (API)

# Install 'sechm' in R:

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

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

Datasets:

Chen2017 - Example dataset

On BioConductor:sechm-1.21.0(bioc 3.24)sechm-1.20.0(bioc 3.23)

geneexpression visualization

7.29 score 8 stars 2 packages 202 scripts 12 exports 64 dependencies

Last updated from:27f4b8f067. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	186
linux-devel-x86_64	NOTE	330
source / vignettes	OK	251
linux-release-x86_64	NOTE	295
macos-release-arm64	NOTE	152
macos-oldrel-arm64	NOTE	135
windows-devel	NOTE	200
windows-release	NOTE	206
windows-oldrel	NOTE	202
wasm-release	OK	167

Exports:crossHm getBreaks getDEA getDEGs log2FC meltSE resetAllSechmOptions safescale sechm setRowAttr setSechmOption sortRows

Dependencies:abind Biobase BiocGenerics ca circlize cli clue cluster codetools colorspace ComplexHeatmap crayon curl DelayedArray digest doParallel farver foreach gclus generics GenomicRanges GetoptLong GlobalOptions glue IRanges iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv nlme permute png qap R6 randomcoloR RColorBrewer Rcpp registry rjson rlang Rtsne S4Arrays S4Vectors scales Seqinfo seriation shape SparseArray stringi stringr SummarizedExperiment TSP V8 vctrs vegan viridisLite XVector

sechm

Rendered fromsechm.Rmdusingknitr::rmarkdown

Last update: 2023-09-25
Started: 2021-04-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
crossHm	crossHm
Example dataset	Chen2017 data
getBreaks	getBreaks
getDEA	getDEA
Get DEGs from a SE or list of DEA results	getDEGs
homogenizeDEA	homogenizeDEA
log2FC	log2FC
meltSE	meltSE
qualitativeColors	qualitativeColors
resetAllSechmOptions	resetAllSechmOptions
safescale	safescale
sechm	sechm
Set rowData attribute of given rows	setRowAttr
setSechmOption	setSechmOption
sortRows	sortRows