Package: scMultiome 1.13.2

Xiaosai Yao

scMultiome: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets

Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects.

Authors:Xiaosai Yao [cre, aut], Aleksander Chlebowski [aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz Włodarczyk [aut]

scMultiome_1.13.2.tar.gz
scMultiome_1.13.2.tar.gz(r-4.7-any)scMultiome_1.13.2.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scMultiome/json (API)

# Install 'scMultiome' in R:

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

On BioConductor:scMultiome-1.13.2(data/experiment 3.24)scMultiome-1.12.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

packagetypedata experimenthub singlecelldata expressiondata sequencingdata homo_sapiens_data cellculture tissue geo datapkg

4.29 score 13 scripts 19 exports 93 dependencies

Last updated from:f0adfb38f4. Checks:1 WARNING, 2 ERROR, 1 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	WARNING	200
linux-devel	ERROR	397
source / vignettes	OK	324
linux-release	ERROR	496

Exports:AR_drug assertHDF5 colonHealthy dummyMAE dummySCE hematopoiesis listDatasets loadExp loadMAE PBMC_10x prostateENZ reprogramSeq saveExp saveMAE TEADi_resistance testFile tfBinding tfMotifs uploadFile

Dependencies:abind alabaster.base alabaster.matrix alabaster.schemas AnnotationDbi AnnotationHub askpass assorthead AzureAuth AzureGraph AzureRMR AzureStor backports Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocManager BiocVersion Biostrings bit bit64 blob cachem checkmate cli cpp11 crayon curl DBI dbplyr DelayedArray digest dir.expiry dplyr ExperimentHub fastmap filelock generics GenomicRanges glue h5mread HDF5Array httr httr2 IRanges jose jsonlite jsonvalidate KEGGREST lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment openssl pillar pkgconfig png purrr R6 rappdirs Rcpp rhdf5 rhdf5filters Rhdf5lib rlang RSQLite S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 uuid V8 vctrs withr xml2 XVector yaml

scMultiome tutorial

Rendered fromscMultiome.Rmdusingknitr::rmarkdown

Last update: 2024-09-26
Started: 2022-12-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AR-dependent gene expression in prostate cancer cells	AR_drug
check if a file is a valid HDF5 file	assertHDF5
Single-cell analysis of samples from healthy human colon	colonHealthy
save and load data sets	fileOperations loadExp loadMAE saveExp saveExp,SingleCellExperiment-method saveExp,SummarizedExperiment-method saveMAE testFile uploadFile
scATAC-seq and unpaired scRNA-seq of hematopoetic cells	hematopoiesis
list all available data sets	listDatasets
10k PBMC data	PBMC_10x
LNCaP Cells Treated with Enzalutamide	prostateENZ
reprogramSeq	reprogramSeq
TEAD inhibitor resistance	TEADi_resistance
documentation templates	makeMakeData makeMakeMetadata makeR templates
TF Binding Info	tfBinding
Transcription factor motifs	tfMotifs