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PeteHaitch / MethylSeqData

Collection of Public DNA Methylation Sequencing Datasets
https://bioconductor.org/packages/MethylSeqData/
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Potential datasets #1

Open PeteHaitch opened 4 years ago

PeteHaitch commented 4 years ago

Dump of datasets that may be useful.

PeteHaitch commented 4 years ago

There are thousands of samples available through DeepBlue.

library(DeepBlueR)
#> Loading required package: XML
#> Loading required package: RCurl
#> Welcome to the DeepBlueR package
#> DeepBlue is online

mC_experiments <- deepblue_list_experiments(epigenetic_mark = "DNA Methylation")
#> Called method: deepblue_list_experiments
#> Reported status was: okay
mC_experiments
#>            id                           name
#>    1: e107450         HPC8_cpg.rate.bedgraph
#>    2:  e47152                    ENCFF257GGV
#>    3:  e46670                    ENCFF001ZIA
#>    4: e107453        HPC28_cpg.rate.bedgraph
#>    5: e107445        HPC20_cpg.rate.bedgraph
#>   ---                                       
#> 2086: e100273        NK_PB_I44_covg.bedgraph
#> 2087: e100271   MLP1_PB_I7_fracmeth.bedgraph
#> 2088: e100270 Bcell_PB_I53_fracmeth.bedgraph
#> 2089: e100272         MK_BM_I1_covg.bedgraph
#> 2090: e100269       HSC_PB_I31_covg.bedgraph

Created on 2020-08-17 by the reprex package (v0.3.0)

I believe these are only for a single sample, so we could collate these into useful sets à la celldex.