Package: CTdata 1.5.0

Laurent Gatto

CTdata: Data companion to CTexploreR

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

Authors:Axelle Loriot [aut], Julie Devis [aut], Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths, cre]

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

# Install 'CTdata' in R:

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

Bug tracker:https://github.com/uclouvain-cbio/ctdata/issues

On BioConductor:CTdata-1.5.0(bioc 3.20)CTdata-1.4.0(bioc 3.19)

bioconductor-package

14 exports 1.24 score 60 dependencies 1 dependents

Last updated 2 months agofrom:a0144cb246

Exports:CCLE_correlation_matrix CCLE_data CT_genes CT_mean_methylation_in_tissues CT_methylation_in_tissues CTdata DAC_treated_cells DAC_treated_cells_multimapping GTEX_data normal_tissues_multimapping_data scRNAseq_HPA TCGA_CT_methylation TCGA_TPM testis_sce

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

Cancer Testis Datasets

Julie Devis, Laurent Gatto, Axelle Loriot

Rendered fromCTdata.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-08-16
Started: 2023-02-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Gene correlations in CCLE cancer cell lines	CCLE_correlation_matrix
Genes expression data in CCLE	CCLE_data
CT genes description table	CT_genes
CT genes' promoters mean methylation	CT_mean_methylation_in_tissues
Methylation of CpGs within CT promoters	CT_methylation_in_tissues
All CTdata datasets	CTdata
DE genes with/without demethylating agent	DAC_treated_cells
DE genes treated or not with a demethylating agent	DAC_treated_cells_multimapping
Genes expression in GTEX	GTEX_data
A short function that returns the default CTdata tags and, if provided, additional data-specific tags.	makeTags
Gene expression values in normal tissues	normal_tissues_multimapping_data
Gene expression in human cell types	scRNAseq_HPA
Methylation of CT promoters in TCGA samples	TCGA_CT_methylation
Gene expression in TCGA samples	TCGA_TPM
Testis scRNAseq data	testis_sce