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Nothing in the usage indicates that the name provided through the -n option must not include spaces or that it can't be quoted to include spaces. The error message also isn't really explicit here eith…
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cbImportSeurat2 fails when run on a conda install due to the R script not being installed:
```
Fatal error: Exit code 1 ()
INFO:root:inFname: seurat.rds, outDir: output, datasetName: output
Trac…
pcm32 updated
5 years ago
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I have a quickGenes.csv file. In the first column, I've placed the gene name and in the second column, I've placed the description. After running cbBuild, the genes show up in the 'Dataset genes' sect…
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Full error message:
```
Regressing out percent_mito and number of UMIs
Traceback (most recent call last):
File "/cluster/home/mspeir/miniconda3/bin/cbScanpy", line 10, in
sys.exit(cbScanpy…
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When working with large single-cell datasets, it is often useful to look at two or more levels. Several papers have done analysis at two or more levels:
- Level 1: PCA and tSNE on the full set of a…
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Seriously dude, unit testing.
`cellbrowser/convert.py`
typo in line 34: line should be line1
```
elif line1.startswith("Gene ID"):
if "Cluster 1 Weight" in line:
fields…
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When I run `cbMarkerAnnotate` through my miniconda3 install, I get the error:
```
Traceback (most recent call last):
File "/cluster/home/mspeir/miniconda3/bin/cbMarkerAnnotate", line 6, in
…
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1. Go to https://hgwdev.gi.ucsc.edu/~mspeir/cb_demo/?ds=Quake_Glioblastoma_GSE84465
2. Under 'Color by annotation', click into the search box
3. Type 'ercc'
4. Notice it says 'no matches'
5. Scrol…
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Pieris requested to have the final dataset browseable through a web interface to make it accessible to non-bioinformatics researchers.
I'll have to collect more information about what features the…
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Example, I updated the summary.html for a dataset and then ran cbBuild. I expected that the new summary.html would overwrite the old one, but that doesn't seem to be the case.
I had to actually go…