Package: TENxIO 1.9.3
Marcel Ramos
TENxIO: Import methods for 10X Genomics files
Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.
Authors:
TENxIO_1.9.3.tar.gz
TENxIO_1.9.3.zip(r-4.5)TENxIO_1.9.3.zip(r-4.4)TENxIO_1.9.3.zip(r-4.3)
TENxIO_1.9.3.tgz(r-4.4-any)TENxIO_1.9.3.tgz(r-4.3-any)
TENxIO_1.9.3.tar.gz(r-4.5-noble)TENxIO_1.9.3.tar.gz(r-4.4-noble)
TENxIO_1.9.3.tgz(r-4.4-emscripten)TENxIO_1.9.3.tgz(r-4.3-emscripten)
TENxIO.pdf |TENxIO.html✨
TENxIO/json (API)
NEWS
| # Install 'TENxIO' in R: |
| install.packages('TENxIO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/tenxio/issues
On BioConductor:TENxIO-1.9.3(bioc 3.21)TENxIO-1.8.2(bioc 3.20)
softwareinfrastructuredataimportsinglecellbioconductor-package
Last updated 1 months agofrom:c6c5a731f5. Checks:OK: 5 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 22 2024 |
| R-4.5-win | OK | Nov 22 2024 |
| R-4.5-linux | OK | Dec 22 2024 |
| R-4.4-win | OK | Nov 22 2024 |
| R-4.4-mac | ERROR | Dec 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | ERROR | Dec 22 2024 |
Exports:annotationannotation<-decompressgenomeimportmetadatapathrowDatarowRangesshowTENxFileTENxFileListTENxFragmentsTENxH5TENxMTXTENxPeaksTENxTSV
Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsBiocIObitbit64bitopsclicliprcpp11crayoncurlDelayedArrayfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueHDF5ArrayhmshttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogressR.methodsS3R.ooR.utilsR6RCurlreadrrhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsSingleCellExperimentSparseArraySummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| TENxFile constructor function | TENxFile |
| TENxFile: General purpose class for 10X files | .TENxFile metadata,TENxFile-method TENxFile-class |
| TENxFileList: Represent groups of files from 10X Genomic | TENxFileList |
| TENxFileList: A list-like representation for TENxFiles | .TENxFileList decompress,TENxFileList-method import,TENxFileList,ANY,ANY-method metadata,TENxFileList-method path,TENxFileList-method TENxFileList-class |
| TENxFragments: Import fragments files from 10X | TENxFragments |
| TENxFragments: A class to represent fragments data as 'GRanges' | .TENxFragments import,TENxFragments,ANY,ANY-method TENxFragments-class |
| TENxH5: Represent H5 files from 10X | TENxH5 |
| TENxH5: The HDF5 file representation class for 10X Data | .TENxH5 dim,TENxH5-method dimnames,TENxH5-method genome,TENxH5-method import,TENxH5,ANY,ANY-method rowData,TENxH5-method rowRanges,TENxH5-method show,TENxH5-method TENxH5-class |
| TENxIO: A Bioconductor package for importing 10X Genomics files | TENxIO-package TENxIO |
| TENxMTX: Represent Matrix Market Format Files from 10X | TENxMTX |
| TENxMTX: The Matrix Market representation class for 10X Data | .TENxMTX import,TENxMTX,ANY,ANY-method TENxMTX-class |
| Import 10x peak annotation files from 10x | TENxPeaks |
| TENxPeaks: The class to represent 10x Peaks files | .TENxPeaks annotation,SingleCellExperiment-method annotation<-,SingleCellExperiment,ANY-method import,TENxPeaks,ANY,ANY-method TENxPeaks-class |
| TENxTSV: A class to represent 10x tab separated values files | .TENxTSV import,TENxTSV,ANY,ANY-method metadata,TENxTSV-method TENxTSV TENxTSV-class |
