Package: sechm 1.15.0

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]

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sechm.pdf |sechm.html
sechm/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:sechm-1.15.0(bioc 3.21)sechm-1.14.0(bioc 3.20)

geneexpressionvisualization

6.77 score 6 stars 2 packages 55 scripts 292 downloads 12 exports 72 dependencies

Last updated 4 months agofrom:adfb618d00. Checks:1 OK, 6 NOTE, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winNOTEJan 29 2025
R-4.5-macWARNINGJan 29 2025
R-4.5-linuxNOTEJan 29 2025
R-4.4-winNOTEJan 29 2025
R-4.4-macNOTEJan 29 2025
R-4.3-winNOTEJan 29 2025
R-4.3-macNOTEJan 29 2025

Exports:crossHmgetBreaksgetDEAgetDEGslog2FCmeltSEresetAllSechmOptionssafescalesechmsetRowAttrsetSechmOptionsortRows

Dependencies:abindaskpassBiobaseBiocGenericscacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcrayoncurlDelayedArraydigestdoParallelfarverforeachgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongGlobalOptionsgluehttrIRangesiteratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpermutepngqapR6randomcoloRRColorBrewerRcppregistryrjsonrlangRtsneS4ArraysS4VectorsscalesseriationshapeSparseArraystringistringrSummarizedExperimentsysTSPUCSC.utilsV8vctrsveganviridisLiteXVector

sechm

Rendered fromsechm.Rmdusingknitr::rmarkdownon Jan 29 2025.

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

Readme and manuals

Help Manual

Help pageTopics
crossHmcrossHm
Example datasetChen2017 data
getBreaksgetBreaks
getDEAgetDEA
Get DEGs from a SE or list of DEA resultsgetDEGs
homogenizeDEAhomogenizeDEA
log2FClog2FC
meltSEmeltSE
qualitativeColorsqualitativeColors
resetAllSechmOptionsresetAllSechmOptions
safescalesafescale
sechmsechm
Set rowData attribute of given rowssetRowAttr
setSechmOptionsetSechmOption
sortRowssortRows