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Thank you for your wonderful work!
I encountered an issue while running mmp_visualization.ipynb. Although I successfully ran MMP and obtained the results, the notebook requires reading an h5_feats_…
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Hi,
I am trying to compute survival plots for a specific set of genes expressed in a specific samples in TCGA.
What I am doing is
```
listSamples
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with the Gene Level Copy Number Scores
Here is my code
all_projects
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We seem to be missing clinical annotation for the TCGA Breast paper:
http://www.cbioportal.org/study.do?cancer_study_id=brca_tcga_pub2015#summary
There should be annotation on ductal vs lobular, as w…
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### Description
in the following table definition, the comma of 3 lines:
is_ffpe text NULL -- is_ffpe; Indicator to signify whether or not the tissue sample was fixed in formalin and embedded i…
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Hi nakul:
Recently, I used the TEprof2 to find some interesting TE-gene chimeric transcripts. But I suspect it may happen in noramal tissue. The STEP12 write "In the case of our publication, we fil…
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lgggbm_tcga_pub ('Merged Cohort of LGG and GBM (TCGA, Cell 2016)') includes data from both LGG & GBM cohorts, so should appear as redundant when any of those are selected. Currently it doesn't get fla…
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This is a persistent error I get (it has not succeeded once):
File "/opt/gdc-bulk-download.py", line 108, in
r = requests.post(URL_BASE + 'data', d…
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Hi,
I am interested in using your ABIS app. Would it be possible to run ABIS (web version) on a large RNA-seg data from TCGA? Till how many samples web version is useful or there is no limit. My sam…
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Hi.
I've run DoAbsolute utilizing the example data. Here present the code.
```
example_path = system.file("extdata", package = "DoAbsolute", mustWork = T)
# segmentation file
seg_normal = fi…