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:
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✨
card.svg |card.png
sechm/json (API)
NEWS
| # 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
- Chen2017 - Example dataset
On BioConductor:sechm-1.21.0(bioc 3.24)sechm-1.20.0(bioc 3.23)
Last updated from:27f4b8f067. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 175 | ||
| linux-devel-x86_64 | NOTE | 306 | ||
| source / vignettes | OK | 255 | ||
| linux-release-x86_64 | NOTE | 320 | ||
| macos-release-arm64 | NOTE | 161 | ||
| macos-oldrel-arm64 | NOTE | 193 | ||
| windows-devel | NOTE | 207 | ||
| windows-release | NOTE | 225 | ||
| windows-oldrel | NOTE | 199 | ||
| wasm-release | OK | 125 |
Exports:crossHmgetBreaksgetDEAgetDEGslog2FCmeltSEresetAllSechmOptionssafescalesechmsetRowAttrsetSechmOptionsortRows
Dependencies:abindBiobaseBiocGenericscacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcrayoncurlDelayedArraydigestdoParallelfarverforeachgclusgenericsGenomicRangesGetoptLongGlobalOptionsglueIRangesiteratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvnlmepermutepngqapR6randomcoloRRColorBrewerRcppregistryrjsonrlangRtsneS4ArraysS4VectorsscalesSeqinfoseriationshapeSparseArraystringistringrSummarizedExperimentTSPV8vctrsveganviridisLiteXVector
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 |
