Package: CTdata 1.7.0

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]

CTdata_1.7.0.tar.gz
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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'))

Peer review:

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

On BioConductor:CTdata-1.7.0(bioc 3.21)CTdata-1.6.0(bioc 3.20)

transcriptomicsepigeneticsgeneexpressiondataimportexperimenthubsoftware

5.69 score 1 stars 1 packages 1 scripts 117 downloads 30 exports 60 dependencies

Last updated 2 months agofrom:0cd0dfabe9. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winOKNov 29 2024
R-4.4-macOKNov 29 2024
R-4.3-winOKNov 29 2024
R-4.3-macOKNov 29 2024

Exports:all_genesCCLE_correlation_matrixCCLE_dataCT_genesCT_mean_methylation_in_tissuesCT_methylation_in_tissuesCTdataDAC_treated_cellsDAC_treated_cells_multimappingembryo_sce_Petropoulosembryo_sce_ZhuFGC_sceGTEX_datahESC_dataHPA_cell_type_specificitiesmean_methylation_in_embryomean_methylation_in_FGCmean_methylation_in_hESCmean_methylation_in_tissuesmethylation_in_embryomethylation_in_FGCmethylation_in_hESCmethylation_in_tissuesnormal_tissues_multimapping_dataoocytes_scescRNAseq_HPATCGA_CT_methylationTCGA_methylationTCGA_TPMtestis_sce

Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrpngpurrrR6rappdirsrlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc

Cancer Testis Datasets

Julie Devis, Laurent Gatto, Axelle Loriot

Rendered fromCTdata.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-09-30
Started: 2023-02-08

Readme and manuals

Help Manual

Help pageTopics
All genes genes description tableall_genes
Gene correlations in CCLE cancer cell linesCCLE_correlation_matrix
Genes expression data in CCLECCLE_data
CT genes description tableCT_genes
CT genes' promoters mean methylationCT_mean_methylation_in_tissues
Methylation of CpGs within CT promotersCT_methylation_in_tissues
All CTdata datasetsCTdata
DE genes with/without demethylating agentDAC_treated_cells
DE genes treated or not with a demethylating agentDAC_treated_cells_multimapping
Embryo scRNAseqembryo_sce_Petropoulos
Embryo scRNAseqembryo_sce_Zhu
Fetal gonad scRNAseqFGC_sce
Genes expression in GTEXGTEX_data
Genes expression in hESChESC_data
Cell type specificities (from HPA)HPA_cell_type_specificities
A short function that returns the default CTdata tags and, if provided, additional data-specific tags.makeTags
All genes' promoters mean methylation in embryosmean_methylation_in_embryo
All genes' promoters mean methylation in FGCmean_methylation_in_FGC
All genes' promoters mean methylation in hESCmean_methylation_in_hESC
All genes' promoters mean methylationmean_methylation_in_tissues
Methylation of CpGs within all genes promoters in embryomethylation_in_embryo
Methylation of CpGs within all genes promoters in FGCmethylation_in_FGC
Methylation of CpGs within all genes promoters in hESCmethylation_in_hESC
Methylation of CpGs within all genes promotersmethylation_in_tissues
Gene expression values in normal tissuesnormal_tissues_multimapping_data
Oocytes scRNAseqoocytes_sce
Gene expression in human cell typesscRNAseq_HPA
Methylation of CT promoters in TCGA samplesTCGA_CT_methylation
Methylation of all genes promoters in TCGA samplesTCGA_methylation
Gene expression in TCGA samplesTCGA_TPM
Testis scRNAseq datatestis_sce