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@hbarsnes @mvaudel @StSchulze
We have continued working with the metadata experimental design.
See example, https://github.com/PRIDE-Archive/pride-metadata-standard/tree/master/experimental-des…
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## ENVIRONMENT
```
OS and Version: Ubuntu 16.04
Python Version: Python 3.6.9
MobSF Version: v2.0.2 Beta
```
## EXPLANATION OF THE ISSUE
```
While downloading json for ipa files…
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I think the ENA scraper might be broken. https://circleci.com/gh/AlexsLemonade/refinebio/15332
```
WARNING:data_refinery_foreman.surveyor.harmony:Cannot determine sample title!
2019-03-25 18:06:5…
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As requested by @lshep: currently, `bfcrpath` prints out a progress bar, which is nice in interactive sessions but annoying when compiling Rmarkdown documents. Ideally this could be turned off - or ev…
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### Context
Jackiecrunch (#466)
### Problem or idea
We are performing some smoothing of the sample metadata and these harmonized values are the ones being displayed in the samples table view.…
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I'm adding that expression atlas downloader now (#489), and wondering where the files should go.
`pbmc68k_reduced` and `toggleswitch` put the datasets relative to where scanpy is installed (via `__…
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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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### Context
Once https://github.com/AlexsLemonade/refinebio/pull/447 lands, we should be able to do the following identifier conversions for submitter-processed data:
* Illumina BeadArray: Probe…
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To keep the prototype I'm building is consistent with the data available/extractable in the back end, here are the experiment fields(unordered):
- Abstract
- Publication and link to publication
- S…
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I have a PR coming for the reheadering which will fix the vcf reheadering. I am however getting this error:
```
[varscan.snp.genome.wustl.edu.TCGA-W5-AA33.vcf] VCF header validation error: SAMPLE hea…