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:
sechm_1.15.0.tar.gz
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sechm_1.15.0.tgz(r-4.4-any)sechm_1.15.0.tgz(r-4.3-any)
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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')) |
Bug tracker:https://github.com/plger/sechm/issues
- Chen2017 - Example dataset
On BioConductor:sechm-1.15.0(bioc 3.21)sechm-1.14.0(bioc 3.20)
Last updated 2 months agofrom:adfb618d00. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:crossHmgetBreaksgetDEAgetDEGslog2FCmeltSEresetAllSechmOptionssafescalesechmsetRowAttrsetSechmOptionsortRows
Dependencies:abindaskpassBiobaseBiocGenericscacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcrayoncurlDelayedArraydigestdoParallelfarverforeachgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongGlobalOptionsgluehttrIRangesiteratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpermutepngqapR6randomcoloRRColorBrewerRcppregistryrjsonrlangRtsneS4ArraysS4VectorsscalesseriationshapeSparseArraystringistringrSummarizedExperimentsysTSPUCSC.utilsV8vctrsveganviridisLiteXVectorzlibbioc
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 |
