ENCODExplorer seems like a really neat way to query and download ENCODE data, however I'm finding it doesn't return data that exists according to the ENCODE website, e.g.
queryEncode(biosample = "ES-E14", target = "CTCF", file_format = "bed", assay = "ChIP-seq", organism = "Mus musculus", fixed = FALSE)
returns NULL, although here there are three bed files available for download.
Sorry for the delay in the answer, I was out of town.
I'd like to add some point to Mike's answers.
About the usage of the `|` in a queryEncode call. The function was not meant to deal with boolean operators. But this is something I think would be interesting to add support for. I created an Issue and will try to add this for the next release.
About the snapshots. We plan to update the snapshot before the next Bioconductor release, and every subsequent release afterward. One of the problem we encountered is that there were some changes in the ENCODE database (for instance, the Roadmap Epigenomics datasets are now availble). We will have to update some part of the code to make sure we update all the metadata correctly. Right now, we do not plan on adding snapshots between release.
Oh, that is interesting that it doesn't actually support the Boolean operators - using `|` works quite well considering that! I'd strongly support adding official support for this - it's useful to be able to search for multiple cell lines and targets at once, and the alternative is nested for loops which is not very nice :)
I agree that it would make a lot of sense. And it should not be such a big change. But I have to prepare a test suite before adding it officially in the documentation/vignettes. I will also have to solve the ^ problem mentionned by Mike that is only applied to the first term.