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Edit by Dandelion Sprout 25th of February 2020: GitHub spectacularly failed to tell me that there was a comment limit of 2,500 comments in issue threads?! So now it seems that discussion has been forc…
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For a new data set how do you make ref in data(ref) ?
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Perform feature data normalization on the positive polarity data. This should include:
- quality assessment based on feature abundances (RSD, RLA)
- injection order dependent signal drift adjustment…
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Hello,
I seems current estimateCellCounts function does not support EPIC array. Is it possible that future version will add this feature or the algorithm itself may not work for EPIC array at all (e.…
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Currently (in Cell 11 of [`2.TCGA-process.ipynb`](https://github.com/cognoma/cancer-data/blob/master/2.TCGA-process.ipynb)), we retain only `Primary Solid Tumor` and `Primary Blood Derived Cancer - Pe…
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Hi,
I was trying to use minfi to estimate cell counts for illumina EPIC data. I upgraded both R and bioconductor, but couldn't execute estimateCellCounts because package "FlowSorted.Blood.EPIC" could…
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Hi!
Thanks so much for your work first of all. This is a really nice repository with really clear instructions and fantastic readability so it's been a pleasure to work with so far!
I'm trying t…
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Samples on ArrayExpress have meta-information in `sdrf` files. We may want to turn some of this information into structured/harmonized fields on our sample table, and to define some harmony with sampl…
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There are several processing steps that go into getting a data set ready for BEAST. These are automated in CFT, but given that we want to try variants we have to do them by hand.
#### Install depen…
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Hello,
I've set up scanpy and tried to reproduce the minimal_examples notebook to begin with. This did not go well from the command line - `sc.settings.set_figure_params(dpi=80)` resulted in python…