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Hi, I'm seeing a parsing error for `brca_tcga_pan_can_atlas_2018`:
`utils::read.table` chokes too easily on malformed files -- is it worth considering switching to readr/vroom or data.table here to…
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Prof.Wang, Can you provide the version information with gene symbol?
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Some examples here: https://arax.ncats.io/beta/?r=36527
example edge attribute list containing the attribute of interest:
```
--
attribute_type_id: | biolink:aggregator_knowledge_source
value_t…
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I found one problem when I tried to download the data:
Error in dplyr::bind_rows(): ! Can't combine ..368$Tumor_Seq_Allele2 and ..369$Tumor_Seq_Allele2 .
Whether is this a problem in the GDC …
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From the publication worldwide shows that BRAF V600E is most common point mutation, but recently I worked on the TCGA dataset, all V600E were converted to V640E which is so different from the data in …
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Hi, ViLa-MIL is quite inspiring. I am curious to know when the code and data will be made available? Thanks.
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Hi, again.
I was able to solve issues with running BayesPrism thanks to your help.
Now I have been using both CIBERSORTx and BayesPrism to analyze various TCGA data with single-cell matrix of my…
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``` r
data("breast.TCGA")
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna,
protein = breast.TCGA$data.train$protein)
# set number of variables to s…
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Hi,
I am trying to recompute IMPRES score for the TCGA samples. I downloaded "SKCM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data.txt" from Broad GDAC Firehose…
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I received the following error today:
Error in GDCquery(project = "TCGA-READ", data.category = "Transcriptome Profiling", :
Please set a valid workflow.type argument from the list below:
Al…