Package: homosapienDEE2CellScore 1.9.0

Justin Marsh

homosapienDEE2CellScore: Example Data Package for CellScore

This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore.

Authors:Justin Marsh [aut, cre]

homosapienDEE2CellScore_1.9.0.tar.gz
homosapienDEE2CellScore_1.9.0.tar.gz(r-4.7-any)homosapienDEE2CellScore_1.9.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
homosapienDEE2CellScore/json (API)

# Install 'homosapienDEE2CellScore' in R:

install.packages('homosapienDEE2CellScore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/flaviusb/homosapiendee2cellscore/issues

On BioConductor:homosapienDEE2CellScore-1.9.0(data/experiment 3.24)homosapienDEE2CellScore-1.8.0(data/experiment 3.23)

rnaseqdata genome experimenthub expressiondata datapkg

3.00 score 3 scripts 16 exports 91 dependencies

Last updated from:38461f61c7. Checks:1 NOTE, 2 WARNING, 1 ERROR. 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	NOTE	195
linux-devel	WARNING	533
source / vignettes	ERROR	286
linux-release	WARNING	421

Exports:buildData buildRaw cols downloadAllTheData HomosapienDEE2_QC_PASS_Agg HomosapienDEE2_QC_PASS_Deseq2 HomosapienDEE2_QC_PASS_Rank HomosapienDEE2_QC_PASS_Raw HomosapienDEE2_QC_WARN_Agg HomosapienDEE2_QC_WARN_Deseq2 HomosapienDEE2_QC_WARN_Rank HomosapienDEE2_QC_WARN_Raw readInSEFolder readInSEZip srx_agg_se writeOutSEZip

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 dplyr ExperimentHub farver fastmap filelock formatR futile.logger futile.options generics GenomicRanges getDEE2 ggplot2 glue gtable htm2txt httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang RSQLite Rtsne S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
buildData builds the data included in this package	buildData
buildRaw gets the raw data in SummarizedExperiment format	buildRaw
hsapiens column data we are targetting	cols
downloadAllTheData in SummarizedExperiment format	downloadAllTheData
Automatically created ergonomic accessor functions	HomosapienDEE2_QC_PASS_Agg HomosapienDEE2_QC_PASS_Deseq2 HomosapienDEE2_QC_PASS_Rank HomosapienDEE2_QC_PASS_Raw HomosapienDEE2_QC_WARN_Agg HomosapienDEE2_QC_WARN_Deseq2 HomosapienDEE2_QC_WARN_Rank HomosapienDEE2_QC_WARN_Raw
readInSEFolder read a SummarizedExperiment in from a folder	readInSEFolder
readInSEZip read a SummarizedExperiment in from a zip file	readInSEZip
srx_agg_se is a version of srx_agg that works on SummarizedExperiments	srx_agg_se
writeOutSEZip writes out a SummarizedExperiment into a zip file	writeOutSEZip