Package: scTGIF 1.21.0
Koki Tsuyuzaki
scTGIF: Cell type annotation for unannotated single-cell RNA-Seq data
scTGIF connects the cells and the related gene functions without cell type label.
Authors:
scTGIF_1.21.0.tar.gz
scTGIF_1.21.0.zip(r-4.5)scTGIF_1.21.0.zip(r-4.4)scTGIF_1.21.0.zip(r-4.3)
scTGIF_1.21.0.tgz(r-4.4-any)scTGIF_1.21.0.tgz(r-4.3-any)
scTGIF_1.21.0.tar.gz(r-4.5-noble)scTGIF_1.21.0.tar.gz(r-4.4-noble)
scTGIF_1.21.0.tgz(r-4.4-emscripten)scTGIF_1.21.0.tgz(r-4.3-emscripten)
scTGIF.pdf |scTGIF.html✨
scTGIF/json (API)
NEWS
| # Install 'scTGIF' in R: |
| install.packages('scTGIF', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- DistalLungEpithelium - Gene expression matrix of DistalLungEpithelium dataset containing five cluster.
- label.DistalLungEpithelium - Cellular label of DistalLungEpithelium dataset containing five cluster.
- pca.DistalLungEpithelium - The result of PCA of the DistalLungEpithelium dataset.
On BioConductor:scTGIF-1.21.0(bioc 3.21)scTGIF-1.20.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dimensionreductionqualitycontrolsinglecellsoftwaregeneexpression
Last updated 2 months agofrom:90a5f4e22d. 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:calcTGIFcellMarkerToGmtconvertRowIDreportTGIFsettingTGIF
Dependencies:abindannotateAnnotationDbiaskpassbabelgenebase64encBiobaseBiocGenericsBiocManagerBiocStyleBiostringsbitbit64blobbookdownbslibcachemclassclassIntcliclustercolorspaceconcavemancpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdotCall64dplyre1071entropyevaluatefansifarverfastmapfieldsfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2gluegraphGSEABasegtablehexbinhighrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglaterlatticelazyevallifecyclemagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemisc3dmsigdbrmunsellnlmennTensoropensslpillarpkgconfigplogrplot3DplotlypngpolyclippromisesproxypurrrR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownRSQLiterTensors2S4ArraysS4VectorssassscalesschexsfSingleCellExperimentspamSparseArraystringistringrSummarizedExperimentsyssystemfontstagcloudtibbletidyrtidyselecttinytextweenrUCSC.utilsunitsutf8V8vctrsviridisLitewithrwkxfunXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cell type annotation for unannotated single-cell RNA-Seq data | scTGIF-package scTGIF |
| Function for connecting cellular patterns and functional patterns using jNMF | calcTGIF calcTGIF,SingleCellExperiment-method |
| A function to convert the CellMarker data to GMT files. | cellMarkerToGmt |
| A function to change the row names of a matrix. | convertRowID |
| Gene expression matrix of DistalLungEpithelium dataset containing five cluster. | DistalLungEpithelium |
| Cellular label of DistalLungEpithelium dataset containing five cluster. | label.DistalLungEpithelium |
| The result of PCA of the DistalLungEpithelium dataset. | pca.DistalLungEpithelium |
| Function for reporting the result of 'calcTGIF' function | reportTGIF reportTGIF,SingleCellExperiment-method |
| Paramter setting for scTGIF | settingTGIF settingTGIF,SingleCellExperiment-method |
