Package: TENxIO 1.7.4

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]

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TENxIO.pdf |TENxIO.html✨
TENxIO/json (API)
NEWS

# Install 'TENxIO' in R:

install.packages('TENxIO', repos = c('https://link-ny.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:TENxIO-1.7.3(bioc 3.20)TENxIO-1.6.1(bioc 3.19)

software infrastructure dataimport singlecell bioconductor-package

16 exports 1.64 score 59 dependencies 1 dependents 6 scripts

Last updated 5 days agofrom:172f383539. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Sep 11 2024
R-4.5-win	NOTE	Sep 11 2024
R-4.5-linux	NOTE	Sep 11 2024
R-4.4-win	OK	Sep 11 2024
R-4.4-mac	ERROR	Sep 11 2024
R-4.3-win	OK	Sep 11 2024
R-4.3-mac	ERROR	Sep 11 2024

Exports:annotation annotation<-decompress genome import path rowData rowRanges show TENxFile TENxFileList TENxFragments TENxH5 TENxMTX TENxPeaks TENxTSV

Dependencies:abind askpass Biobase BiocBaseUtils BiocGenerics BiocIO bit bit64 bitops cli clipr cpp11 crayon curl DelayedArray fansi GenomeInfoDb GenomeInfoDbData GenomicRanges glue hms httr IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig prettyunits progress R.methodsS3 R.oo R.utils R6 RCurl readr rlang S4Arrays S4Vectors SingleCellExperiment SparseArray SummarizedExperiment sys tibble tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XVector zlibbioc

TENxIO: Import Single Cell Data Files

Marcel Ramos

Rendered fromTENxIO.Rmdusingknitr::rmarkdownon Sep 11 2024.

Last update: 2024-06-05
Started: 2022-08-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
TENxFile constructor function	TENxFile
TENxFile: General purpose class for 10X files	.TENxFile 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 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 TENxTSV TENxTSV-class