Package: TENxIO 1.9.2

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:Marcel Ramos [aut, cre]

TENxIO_1.9.2.tar.gz
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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'))

Peer review:

Bug tracker:https://github.com/waldronlab/tenxio/issues

On BioConductor:TENxIO-1.9.0(bioc 3.21)TENxIO-1.8.0(bioc 3.20)

softwareinfrastructuredataimportsinglecellbioconductor-package

5.59 score 2 packages 7 scripts 110 downloads 17 exports 64 dependencies

Last updated 8 days agofrom:7ba4097662. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winWARNINGNov 14 2024
R-4.5-linuxWARNINGNov 14 2024
R-4.4-winWARNINGNov 14 2024
R-4.4-macERRORNov 14 2024
R-4.3-winWARNINGNov 14 2024
R-4.3-macERRORNov 14 2024

Exports:annotationannotation<-decompressgenomeimportmetadatapathrowDatarowRangesshowTENxFileTENxFileListTENxFragmentsTENxH5TENxMTXTENxPeaksTENxTSV

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsBiocIObitbit64bitopsclicliprcpp11crayoncurlDelayedArrayfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueHDF5ArrayhmshttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogressR.methodsS3R.ooR.utilsR6RCurlreadrrhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsSingleCellExperimentSparseArraySummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXVectorzlibbioc

TENxIO: Import Single Cell Data Files

Marcel Ramos

Rendered fromTENxIO.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-10-17
Started: 2022-08-24

Readme and manuals

Help Manual

Help pageTopics
TENxFile constructor functionTENxFile
TENxFile: General purpose class for 10X files.TENxFile metadata,TENxFile-method TENxFile-class
TENxFileList: Represent groups of files from 10X GenomicTENxFileList
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 10XTENxFragments
TENxFragments: A class to represent fragments data as 'GRanges'.TENxFragments import,TENxFragments,ANY,ANY-method TENxFragments-class
TENxH5: Represent H5 files from 10XTENxH5
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 filesTENxIO-package TENxIO
TENxMTX: Represent Matrix Market Format Files from 10XTENxMTX
TENxMTX: The Matrix Market representation class for 10X Data.TENxMTX import,TENxMTX,ANY,ANY-method TENxMTX-class
Import 10x peak annotation files from 10xTENxPeaks
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