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I'm curious what you recommend for sequencing data that has some inserts that are shorter than 2x the read length such that some genomic bases are read in both R1 and R2?
I believe I am seeing case…
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Hi everyone, if people aren't yet sick of discussing the finer points of GFA implementation, I've got another one! I like the concept of paths in an assembly graph and use them a lot in Bandage, so I'…
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Dear all, hi Pete,
I observed, that the selection of Annotations or Objects in scripting does not work anymore after the line:
mergeSelectedAnnotations();
If this line is followed by selec…
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Will be this be correct way to the `testing.py`
```
if __name__ == '__main__':
run_test_case(0,"./data_test")
```
where `./data_test` is the name to the `out_dir` where the `prediction.nii.…
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Hey Guys!
I try to define cells into tumor and non-tumor cells with the detection classifier and determine afterwards the positive and negative cells in the respective class (with help of positive ce…
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I most commonly analyze multiple slides at one time -- what sort of script could I use to take specific measurements out of each individual slide and put them all together in a single spreadsheet?
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Dave Spencer will provide a list of 10 or so samples for an initial implementation of PON. List will be provided via @dufeiyu
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I'd like to use QuPath to generate training data for a deep learning model. I am annotating various features (let's say, tumor and stroma), and generating tiles within the annotated regions via Analyz…
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So far I have figured out how to detect cells in my TMA, make classifiers and "train" them and get the results outputted nicely from it.
However I would love to make cell detections withing differen…
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The bar should be in the middle of points, why it is way below the middle?
[3S12-075080FM_S3_sorted_mkDup_sorted2-scatter.pdf](https://github.com/etal/cnvkit/files/836125/3S12-075080FM_S3_sorted_mkDu…