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I have 3 datasets from 3 glioblastoma patients in an object that's been through the entire pipeline. From correlating genes loaded on factors with the cluster assignments, it looks like tumor cells an…
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Dear Bcbio team,
I want to add this flag (--f1r2-tar-gz) to the caller mutect2 in my variant.yaml file.
Here's how i've done it.
details:
- algorithm:
aligner: false
mark_duplicates…
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We want to persist the expand/collapse action of groups in the provenance (see https://github.com/datavisyn/tdp_core/issues/378). The `LocalDataProvider.EVENT_GROUP_AGGREGATION_CHANGED` event provides…
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I've increased the [description column](https://www.synapse.org/#!Synapse:syn21895659/tables/) to 1000 chars, but some new descriptions are way over that limit in the merged datasets table:
```
1 …
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Hello,
From the issues I read about this it could be due to having an old version of the package, but I checked and I think I have the newest version: infercnv_1.3.6
I also attach my sessionInfo …
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**Describe the bug**
The downloadable model for the Survival Index prediction does not load within captk.
I get the following error:
"The given SVM model directory does not have all the model …
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For the following data set, I cannot find the journal article or anything to go along with it:
"Study: Single cell RNA-seq of adult and pediatric glioblastoma."
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#### Scientific goals
Identify samples that have _TP53_ or _NF1_ inactivation using gene expression data.
#### Proposed methods
* This would use a pre-existing classifier (trained on TC…
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Leverage ```getTSNEplot.R``` for comparative analysis of harmonized TCGA expression data vs PNOC-0008.
Key plots to be included in patient clinical reports:
1) tSNE of adult TCGA high grade gliom…
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I have a data set of one dependent categorical and 7 categorical features with 12987 samples
I tried one hot encoding and it worked by it is not dealing with these large categories. In addition, I wa…