Package: scaeData 1.8.0

Ahmad Al Ajami

scaeData: Data Package for SingleCellAlleleExperiment

Contains default datasets used by the Bioconductor package SingleCellAlleleExperiment. The raw FASTQ files were sourced from publicly accessible datasets provided by 10x Genomics. Subsequently, our scIGD snakemake workflow was employed to process these FASTQ files. The resulting output from scIGD constitutes to the contents of this data package.

Authors:Ahmad Al Ajami [aut, cre], Jonas Schuck [aut], Federico Marini [aut], Katharina Imkeller [aut]

scaeData_1.8.0.tar.gz
scaeData_1.8.0.tar.gz(r-4.7-any)scaeData_1.8.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scaeData/json (API)

# Install 'scaeData' in R:

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

Bug tracker:https://github.com/agimkeller/scigd/issues

On BioConductor:scaeData-1.9.0(data/experiment 3.24)scaeData-1.8.0(data/experiment 3.23)

experimenthub experimentdata homo_sapiens_data singlecelldata datapkg

4.30 score 2 stars 5 scripts 1 exports 57 dependencies

Last updated from:91e094e5f4 (on RELEASE_3_23). Checks:1 NOTE, 3 OK. Indexed: no.

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

Target	Result	Time
bioc-checks	NOTE	170
linux-devel	OK	239
source / vignettes	OK	376
linux-release	OK	260

Exports:scaeDataGet

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fastmap filelock generics glue httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig png purrr R6 rappdirs rlang RSQLite S4Vectors Seqinfo stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

scaeData User Guide

scaeData | Quick Start | Installation | Usage | Session info

Rendered fromscaeData.Rmdusingknitr::rmarkdown

Last update: 2024-05-02
Started: 2024-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Split getter output	demo_dir_file
Build output list per dataset	ehub_out
Get barcode identifiers for pbmc-10k dataset	get_barcodes_10k
Get barcode identifiers for pbmc-20k dataset	get_barcodes_20k
Get barcode identifiers for pbmc-5k dataset	get_barcodes_5k
Get quantification matrix for pbmc-10k dataset	get_counts_10k
Get quantification matrix for pbmc-20k dataset	get_counts_20k
Get quantification matrix for pbmc-5k dataset	get_counts_5k
Get feature identifiers for pbmc-10k dataset	get_features_10k
Get feature identifiers for pbmc-20k dataset	get_features_20k
Get feature identifiers for pbmc-5k dataset	get_features_5k
Download and process demo dataset	scaeDataGet