Package: mitology 1.5.1
Stefania Pirrotta
mitology: Study of mitochondrial activity from RNA-seq data
mitology allows to study the mitochondrial activity throught high-throughput RNA-seq data. It is based on a collection of genes whose proteins localize in to the mitochondria. From these, mitology provides a reorganization of the pathways related to mitochondria activity from Reactome and Gene Ontology. Further a ready-to-use implementation of MitoCarta3.0 pathways is included.
Authors:
mitology_1.5.1.tar.gz
mitology_1.5.1.zip(r-4.7-any)mitology_1.5.1.zip(r-4.6-any)mitology_1.5.1.zip(r-4.5-any)
mitology_1.5.1.tgz(r-4.6-any)mitology_1.5.1.tgz(r-4.5-any)
mitology_1.5.1.tar.gz(r-4.7-any)mitology_1.5.1.tar.gz(r-4.6-any)
mitology_1.5.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mitology/json (API)
| # Install 'mitology' in R: |
| install.packages('mitology', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/caluralab/mitology/issues
- MitoGenesDB - Mitochondrial genes
- ovse - Example expression data.
On BioConductor:mitology-1.5.0(bioc 3.24)mitology-1.4.0(bioc 3.23)
geneexpressionrnaseqvisualizationsinglecellspatialpathwaysreactomego
Last updated from:4c6814ba32. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 332 | ||
| linux-devel | WARNING | 481 | ||
| source / vignettes | ERROR | 427 | ||
| linux-release | WARNING | 347 | ||
| macos-release | WARNING | 303 | ||
| macos-oldrel | WARNING | 198 | ||
| windows-devel | WARNING | 325 | ||
| windows-release | WARNING | 341 | ||
| windows-oldrel | WARNING | 229 | ||
| wasm-release | OK | 248 |
Exports:enrichMitogetGeneSetsgseaMitomitoHeatmapmitoTreeHeatmapmitoTreePoint
Dependencies:aisdkAnnotationDbiapeaplotaskpassbase64encBiobaseBiocBaseUtilsBiocGenericsBiostringsbitbit64blobbslibcachemcallrcirclizecliclueclusterclusterProfilercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDBIdigestdir.expirydoParallelDOSEdplyrenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachfsgdtoolsgenericsGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablehighrhtmltoolshtmlwidgetshttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelazyevallifecyclemagrittrMASSMatrixmatrixStatsmemoisemimenlmeopensslorg.Hs.eg.dbotelpatchworkpillarpkgconfigplyrpngpolyclipprocessxpspurrrqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreactome.dbReactomePAreshape2rjsonrlangrmarkdownRSQLiteS4VectorsS7sassscalesscatterpieSeqinfoshapestringistringrsyssystemfontstibbletidydrtidygraphtidyrtidyselecttidytreetinytextreeiotweenrutf8vctrsviridisviridisLitewithrxfunXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Mitochondrial Enrichment Analysis of a gene list. | enrichMito |
| Get the mitochondrial gene sets | getGeneSets |
| Mitochondrial GSEA of a gene list. | gseaMito |
| Mitochondrial genes | MitoGenesDB |
| Heatmap of mitochondrial gene sets. | mitoHeatmap |
| Circular heatmap on mitochondrial gene set tree. | mitoTreeHeatmap |
| Circular dotplot on mitochondrial gene set tree. | mitoTreePoint |
| Example expression data. | ovse |