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waldronlab / curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
https://bioconductor.org/packages/curatedTCGAData
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Date of data generation #57

Closed adomingues closed 1 year ago

adomingues commented 1 year ago

Hi all,

I am trying to extract the rrpa data for several of the cohorts but noticed in the files names that the data generation time seems a bit old (20160128):

curatedTCGAData("acc", version = "2.1.0")
snapshotDate(): 2023-04-24
See '?curatedTCGAData' for 'diseaseCode' and 'assays' inputs
    ah_id                                 title file_size                 rdataclass rdatadateadded rdatadateremoved
1  EH4737                   ACC_CNASNP-20160128    0.8 Mb           RaggedExperiment     2021-01-27             <NA>
2  EH4738                   ACC_CNVSNP-20160128    0.2 Mb           RaggedExperiment     2021-01-27             <NA>
3  EH4740         ACC_GISTIC_AllByGene-20160128    0.2 Mb       SummarizedExperiment     2021-01-27             <NA>
4  EH4741             ACC_GISTIC_Peaks-20160128      0 Mb RangedSummarizedExperiment     2021-01-27             <NA>
5  EH4742 ACC_GISTIC_ThresholdedByGene-20160128    0.2 Mb       SummarizedExperiment     2021-01-27             <NA>
6  EH4744       ACC_Methylation-20160128_assays  239.2 Mb       SummarizedExperiment     2021-01-27             <NA>
7  EH4745           ACC_Methylation-20160128_se      6 Mb           RaggedExperiment     2021-01-27             <NA>
8  EH4747                 ACC_Mutation-20160128    0.7 Mb       SummarizedExperiment     2021-01-27             <NA>
9  EH4748              ACC_RNASeq2Gene-20160128    2.7 Mb       SummarizedExperiment     2021-01-27             <NA>
10 EH4750                ACC_RPPAArray-20160128    0.1 Mb       SummarizedExperiment     2021-01-27             <NA>
11 EH8118             ACC_miRNASeqGene-20160128    0.2 Mb       SummarizedExperiment     2023-04-24             <NA>
12 EH8119          ACC_RNASeq2GeneNorm-20160128    5.4 Mb       SummarizedExperiment     2023-04-24             <NA>

So my question is if curatedTCGAData provides access to the latest data available in TCGA (within reason)?

Thank you for proving such a wonderful package!

LiNk-NY commented 1 year ago

Hi @adomingues It provides data from the GDAC Firehose pipeline whose last run was in 2016. For more recently harmonized data, see the GenomicDataCommons package and/or https://portal.gdc.cancer.gov/ Best, Marcel

adomingues commented 1 year ago

Thanks @LiNk-NY! I was already exploring GenomicDataCommons and have a question about it, but I will use the bioconductor forum for that