"Title","Description","BiocVersion","Genome","SourceType","SourceUrl","SourceVersion","Species","TaxonomyId","Coordinate_1_based","DataProvider","Maintainer","RDataClass","DispatchClass","RDataPath","Tags"
"GTEX_data","Gene expression data in normal tissues from GTEx database","3.19","hg38","tab","https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz","8","Homo sapiens","9606","TRUE","The Genotype-Tissue Expression","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/GTEX_data.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:NormalTissues"
"CCLE_data","Gene expression data in cancer cell lines from CCLE","3.19","hg38","CSV","https://ndownloader.figshare.com/files/34989922, https://ndownloader.figshare.com/files/35020903","22Q2","Homo sapiens","9606","TRUE","Cancer Cell Line Encyclopedia","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/CCLE_data.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:CancerData:CellLines"
"normal_tissues_multimapping_data","Gene expression values in normal tissues with or without allowing multimapping","3.19","hg38","FASTQ","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/normal_tissues_multimapping_data.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:NormalTissues:Multimapping"
"DAC_treated_cells","Gene expression values in a set of cell lines treated or not with 5-Aza-2'-Deoxycytidine (DAC), a demethylating agent","3.19","hg38","FASTQ","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/DAC_treated_cells.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:CellLines:DemethylatingAgent"
"DAC_treated_cells_multimapping","Gene expression values (multimapping allowed) in a set of cell lines treated or not with 5-Aza-2'-Deoxycytidine (DAC)","3.19","hg38","FASTQ","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/DAC_treated_cells_multimapping.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:CellLines:DemethylatingAgent:Multimapping"
"TCGA_TPM","Gene expression data in TCGA samples","3.19","hg38","TSV","https://portal.gdc.cancer.gov/","36.0","Homo sapiens","9606","TRUE","The Cancer Genome Atlas","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/TCGA_TPM.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:CancerData:TumorSamples"
"CT_methylation_in_tissues","Methylation values of CpGs located within Cancer-Testis promoters in a set of normal tissues","3.17","hg38","BED","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/v2/CT_methylation_in_tissues.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:CancerTestis:NormalTissues"
"CT_mean_methylation_in_tissues","Mean methylation values of all CpGs located within Cancer-Testis (CT) promoters in a set of normal tissues","3.17","hg38","BED","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/v2/CT_mean_methylation_in_tissues.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:CancerTestis:NormalTissues"
"TCGA_CT_methylation","Methylation of CT promoters in TCGA samples","3.17","hg38","TXT","https://portal.gdc.cancer.gov/","36.0","Homo sapiens","9606","TRUE","The Cancer Genome Atlas","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/v2/TCGA_CT_methylation.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:CancerTestis:CancerData:TumorSamples"
"CT_genes","Cancer-Testis (CT) genes description","3.19","hg38","TSV","https://zenodo.org/record/7537824/files/cancermine_collated.tsv?download=1","49","Homo sapiens","9606","TRUE","CancerMine","Axelle Loriot <axelle.loriot@uclouvain.be>","tibble","Rda","CTdata/eh_data/v3/CT_genes.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:CancerTestis:MethylationData:GeneExpression:CancerData:NormalTissues:TumorSamples"
"CCLE_correlation_matrix","Gene correlations in CCLE cancer cell lines","3.19","hg38","CSV","https://ndownloader.figshare.com/files/34989922, https://ndownloader.figshare.com/files/35020903","22Q2","Homo sapiens","9606","TRUE","Cancer Cell Line Encyclopedia","Axelle Loriot <axelle.loriot@uclouvain.be>","matrix","Rda","CTdata/eh_data/v3/CCLE_correlation_matrix.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:CancerTestis:GeneExpression:CancerData:CellLines"
"testis_sce","Testis scRNAseq data","3.19","hg38","FASTQ","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120508","1","Homo sapiens","9606","TRUE","The adult human testis transcriptional cell atlas, Guo et al. 2018","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/v2/testis_sce.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:scRNAseq:testis"
"scRNAseq_HPA","Gene expression profiles in different human cell types based on scRNAseq data from The Human Protein Atlas","3.19","hg38","TSV","https://www.proteinatlas.org/download/rna_single_cell_type.tsv.zip","1","Homo sapiens","9606","TRUE","The Human Protein Atlas","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/v2/scRNAseq_HPA.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:scRNAseq:normalCellTypes"
"all_genes","All genes description, according to the analysis done for CT genes","3.19","hg38","TSV","https://zenodo.org/record/7537824/files/cancermine_collated.tsv?download=1","49","Homo sapiens","9606","TRUE","CancerMine","Axelle Loriot <axelle.loriot@uclouvain.be>","tibble","Rda","CTdata/eh_data/all_genes.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:GeneExpression:CancerData:NormalTissues:TumorSamples"
"FGC_sce","Fetal gonad scRNAseq","3.19","hg38","RDS","https://cellxgene.cziscience.com/collections/661a402a-2a5a-4c71-9b05-b346c57bc451Data","1","Homo sapiens","9606","TRUE","Single-cell roadmap of human gonadal development (Garcia-Alonso, Nature 2022)","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/FGC_sce.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:scRNAseq:FetalCells:Gonad"
"HPA_cell_type_specificities","Cell type specificities (from HPA)","3.19","hg38","TSV","https://www.proteinatlas.org/","23","Homo sapiens","9606","TRUE","The Human Protein Atlas","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/HPA_cell_type_specificities.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneActivation:scRNAseq:testis:normalCellTypes"
"mean_methylation_in_tissues","Mean methylation values of all CpGs located within all (CT) promoters in a set of normal tissues","3.19","hg38","BED","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/mean_methylation_in_tissues.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:NormalTissues"
"methylation_in_tissues","Methylation values of CpGs located within all promoters in a set of normal tissues","3.19","hg38","BED","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/methylation_in_tissues.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:NormalTissues"
"oocytes_sce","Oocytes scRNAseq","3.19","hg38","TXT","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154762","1","Homo sapiens","9606","TRUE","NCBI GEO : Decoding dynamic epigenetic landscapes in human oocytes
            using single-cell multi-omics sequencing (Yan et al. Cell Stem Cell 2021)","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/oocytes_sce.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:scRNAseq:Oocyts:Gonad"
"TCGA_methylation","Methylation of all genes promoters in TCGA samples","3.19","hg38","TSV","https://portal.gdc.cancer.gov/","36.0","Homo sapiens","9606","TRUE","The Cancer Genome Atlas","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/TCGA_methylation.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:CancerData:TumorSamples"
"embryo_sce_Zhu","Gene expression values in early embryo (blastocyst)","3.19","hg38","tab","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81233","1","Homo sapiens","9606","TRUE","Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos (Zhu et al. 2018)","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/embryo_sce_Zhu.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:scRNAseq:embryo"
"embryo_sce_Petropoulos","Gene expression values in early embryo (blastocyst and Morula)","3.19","hg38","TXT","https://www.ebi.ac.uk/biostudies/files/E-MTAB-3929/","1","Homo sapiens","9606","TRUE","Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in
            Human Preimplantation Embryos (Petropulous et al, 2014)","Axelle Loriot <axelle.loriot@uclouvain.be>","SingleCellExperiment","Rda","CTdata/eh_data/embryo_sce_Petropoulos.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:scRNAseq:embryo"
"hESC_data","Gene expression data in human embryonic stem cells","3.19","hg38","FASTQ","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/hESC_data.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:GeneExpression:hESC"
"methylation_in_hESC","Methylation values of CpGs located within all promoters in human embryonic stem cells","3.19","hg38","BED","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/methylation_in_hESC.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:hESC"
"mean_methylation_in_hESC","Mean methylation values of all CpGs located within all promoters in human embryonic stem cells","3.19","hg38","BED","https://www.encodeproject.org/","5","Homo sapiens","9606","TRUE","ENCODE Project","Axelle Loriot <axelle.loriot@uclouvain.be>","SummarizedExperiment","Rda","CTdata/eh_data/mean_methylation_in_hESC.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:hESC"
"methylation_in_FGC","Methylation values of CpGs located within all promoters in fetal germ cells","3.19","hg19","TXT","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107714","1","Homo sapiens","9606","TRUE","Data from Dissecting the epigenomic dynamics of human fetal germ cell
            development at single-cell resolution (Li et al. 2021)","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/methylation_in_FGC.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:FetalGermCells"
"mean_methylation_in_FGC","Mean methylation values of all CpGs located within all promoters in fetal germ cells","3.19","hg19","TXT","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107714","1","Homo sapiens","9606","TRUE","Data from Dissecting the epigenomic dynamics of human fetal germ cell
            development at single-cell resolution (Li et al. 2021)","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/mean_methylation_in_FGC.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:FetalGermCells"
"methylation_in_embryo","Methylation values of CpGs located within all promoters in early embryo","3.19","hg19","BED","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81233","1","Homo sapiens","9606","TRUE","Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos (Zhu et al. 2018)","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/methylation_in_embryo.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:embryo"
"mean_methylation_in_embryo","Mean methylation values of all CpGs located within all promoters in early embryo","3.19","hg19","BED","https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81233","1","Homo sapiens","9606","TRUE","Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos (Zhu et al. 2018)","Axelle Loriot <axelle.loriot@uclouvain.be>","RangedSummarizedExperiment","Rda","CTdata/eh_data/mean_methylation_in_embryo.rda","ExperimentHub:ExperimentData:ReproducibleResearch:RepositoryData:Homo_sapiens_Data:MethylationData:embryo"
