Package: easierData 1.19.0

Oscar Lapuente-Santana

easierData: easier internal data and exemplary dataset from IMvigor210CoreBiologies package

Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license.

Authors:Oscar Lapuente-Santana [aut, cre], Federico Marini [aut], Arsenij Ustjanzew [aut], Francesca Finotello [aut], Federica Eduati [aut]

easierData_1.19.0.tar.gz
easierData_1.19.0.tar.gz(r-4.7-any)easierData_1.19.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
easierData/json (API)

# Install 'easierData' in R:

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

On BioConductor:easierData-1.19.0(data/experiment 3.24)easierData-1.18.0(data/experiment 3.23)

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

rnaseqdata experimenthub reproducibleresearch immunooncologydata cancerdata experimentdata datapkg

4.00 score 10 scripts 12 exports 67 dependencies

Last updated from:3a9b249a40. Checks:3 NOTE, 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	NOTE	130
linux-devel	NOTE	392
source / vignettes	OK	286
linux-release	NOTE	310

Exports:get_cor_scores_genes get_group_lrpairs get_HGNC_annotation get_intercell_networks get_lr_frequency_TCGA get_Mariathasan2018_PDL1_treatment get_opt_models get_opt_xtrain_stats get_scores_signature_genes get_TCGA_mean_pancancer get_TCGA_sd_pancancer list_easierData

Dependencies:abind AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr DelayedArray dplyr ExperimentHub fastmap filelock generics GenomicRanges glue httr httr2 IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png purrr R6 rappdirs rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

easier Data

Intro to easierData | Load easier Data | Session info | References

Rendered fromeasierData.Rmdusingknitr::rmarkdown

Last update: 2021-10-15
Started: 2021-06-29

Help page	Topics
easierData: easier data package	easierData-pkg
Get the list of genes used to define correlated scores of immune response	get_cor_scores_genes
Get the groups of ligand-receptor pairs	get_group_lrpairs
Get the gene symbols approved annotations	get_HGNC_annotation
Get the cancer-specific intercellular networks, including a pan-cancer network	get_intercell_networks
Get the frequency of each ligand-receptor pair feature across the whole TCGA database	get_lr_frequency_TCGA
Get the Mariathasan2018 PD-L1 treatment data	get_Mariathasan2018_PDL1_treatment
Get the cancer-specific model feature parameters	get_opt_models
Get training set cancer-specific features mean and standard deviation	get_opt_xtrain_stats
Get the gene signatures for each score of immune response	get_scores_signature_genes
Get the mean of the TPM expression of each gene across all TCGA cancer types	get_TCGA_mean_pancancer
Get the standard deviation of the TPM expression of each gene across all TCGA cancer types	get_TCGA_sd_pancancer
List the datasets	list_easierData

Package: easierData 1.19.0

easierData: easier internal data and exemplary dataset from IMvigor210CoreBiologies package

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