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I've been using the recent release of the R package TCGAbiolinks to download and analyze TCGA data and I realize that there may be an error in the function TCGAquery_recount2. Trying to download COAD …
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BioC2019 repository: https://github.com/LieberInstitute/recountWorkshop2019
## Deadlines
- [x] May 27: initial draft of workshop, as the vignette of a stand-alone R package in your own GitHub r…
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Hi,
I'm having trouble importing remote BigWig files with `derfinder`, [which internally](https://github.com/lcolladotor/derfinder/blob/5c1cbd412c5787bf2d2d778977e38dd6ae64976d/R/loadCoverage.R#L40…
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VAE training on all of SRA data for recount2 is estimated to take ~2.5 days running on my lab machine (CPU). When running remotely, use [screen](https://www.howtogeek.com/662422/how-to-use-linuxs-scre…
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File paths have a limit of [260 characters (`MAX_PATH`)](https://msdn.microsoft.com/en-us/library/windows/desktop/aa365247(v=vs.85).aspx) on Windows. Compressed folders from Firebrowse have a lot of f…
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Stumbled upon [snaptron](https://twitter.com/GreeneScientist/status/832635971883593728) today and eventually found my way to this [resource](http://snaptron.cs.jhu.edu/data/tcga/).
There are many v…
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Hi,
Currently in BioC release (3.16) and devel (3.17), `recount` is failing. That's because neither the new IDIES location nor AWS are allowing us to read the BigWig files from the web. I manually …
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When we compared the correlation between gene percentiles generated by SOPHIE versus the manually curated dataset [here](https://github.com/greenelab/generic-expression-patterns/blob/master/human_gene…
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Level | Chap | Activity | Packages | Data
|:-------|:-------|:---------------------------------|:-----|:-----|
100 | 2.3 | Introduction to Bioconductor | rtracklayer, Genomi…
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Hi there,
I'd like to know why, for some projects (such as TCGA-DLBC), the query returns only "primary tumor" sample types, despite on TCGA it is also present "blood derived normal". I notice that t…