-
I would appreciate if you can help how to use this code by considering only 8 slices for 3d dataset. As per my understanding I have made changes to following initialization code. I have made changes i…
-
Hi , I have read your paper, the work is awesome. But I'm not quite sure how the model $M_{R_{WHM},R_{tum}}$ was trained. It was trained on the real FLAIR volumes from the SABRE dataset, and the BRATS…
-
FilterMutectCalls failed with
```
java.lang.IllegalArgumentException: beta must be greater than 0 but got -87566.7500301585
```
"this error only comes after the first pass of filtermutectCalls comple…
-
Hi, I'm analyzing a few old TCGA WXS data (done by NimbleGen/hg18 and VCrome/hg19), and all 8 samples have extremely low nhet (0 or 1) and lcn.em is NA. We were suspicious that it might be coverage pr…
-
Dear infercnv developers,
Hi.
I have a problem when using "runCnvAnalysis" function of SPATA2.
So, I would appreciate it if you let me know if there is a solution.
spata_bm1
-
**Version info**
- bcbio version (`bcbio_nextgen.py --version`):1.2.9
- OS name and version (`lsb_release -ds`): Ubuntu 20.04.5 LTS
**To Reproduce**
Exact bcbio command you have used:
```
noh…
-
Hello!
I was running Mesmer to segment whole tumor images (~36k by 42k pixels) on an M60 GPU and I asked for 450G RAM. I have a few questions below and would appreciate any input. (Also I've tried…
-
Hi,
Sorry for posting again.
I didn't manage to use the marker_permutation function.
Here is the error message I get:
Error in `$
Lan-h updated
3 years ago
-
Hi,
I've been exploring your repository and noticed that you've successfully used Xenium datasets in your library. I'm currently working with similar Xenium files and am interested in replicating y…
jw235 updated
5 months ago
-
After doing somatic variant calling, the AD shows that the alternate allele is supported by three to five reads out of typically about eighty reads for almost all of the variants and the patient has a…