NEWS

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CTdata 1.5

CTdata 1.5.3

• Correction of a bug in mean_methylation_in_embryo and mean_methylation_in_FGC datasets
• Vignette update

CTdata 1.5.2

• Correction of an error in the upload

CTdata 1.5.1

• Used more stringent threshold to define genes activated in CCLE cell lines ang in TCGA tumors (TPM > 1 in at least 1% of tumors and cancer cell lines, and TPM > 5 in at least one tumor and cancer cell line)
• Changed selection criteria of testis-specific and testis-preferential genes in GTEX
• Added a slightly more stringent criteria of selection of testis-specific genes when analysing RNAseq data of normal tissues with multimapping
• Minor modifications in selection of genes induced by DAC
• Set TCGA_catgeory in TCGA_TPM to "leaky" when the q75 expression in normal peritumoral TCGA samples is higher than 0.5
• Added HPA_cell_type_specificity (a table giving cell type specificity of each genes based on Human protein Atlas scRNAseq data)
• Added FGC_sce, scRNAseq data of human fetal gonads
• Added oocytes_sce, scRNAseq data of human oocytes
• Changed preliminary CT_list into all_genes_prelim list to add the characterisation to all genes and not only CT in the package
• Changed criteria for testis specificity, including HPA/TCGA/CCLE category in the definition
• Added CT_gene_type column to differentiate CT genes and CT preferential genes
• Included all genes in methylation objects (methylation_in_tissues, mean_methylation_in_tissues and TCGA_methylation)
• Added all_genes containing all the characterisation and analysis for all genes
• Changed the criteria for regulation by methylation, needing DAC induction and methylation in somatic only
• Reordered CT_genes and all_genes
• Changed all documentation
• Added embryo, FGC and hESC data

CTdata 1.5.0

• New devel

CTdata 1.4

CTdata 1.4.0

• New release Bioc 3.19

CTdata 1.1

CTdata 1.1.5

• Assay from CT_methylation_in_tissues() converted from a tibble to a matrix.
• Suggest and load SingleCellExperiment in vignette.
• Update vignette figure.

CTdata 1.1.4

• New data: scRNAseq_HPA and testis_sce.
• Updated data: CT_methylation_in_tissues, CT_mean_methylation_in_tissues, TCGA_CT_methylation, CT_genes and CCLE_correlation_matrix.

CTdata 1.1.3

• Load SummarizedExperiment in vignette.

CTdata 1.1.2

• Suggest SummarizedExperiment.

CTdata 1.1.1

• Only display a small subset of CCLE_correlation_matrix() in the vignette.

CTdata 1.1.0

• New Bioconductor devel release.

CTdata 0.99

CTdata 0.99.0

• Package submission to Biocoductor.