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Hi, As per the paper, both TCGA and CCLE data was normalized using LIMMA-VOOM. However in the code it seems like only TCGA data being normalized. Please let me know which one is correct ?
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Consider the following matters to address when adding the option to use the “full” TCGA patients reference cohort
1. **Use static plots** (instead of interactive ones, in particular those with per-…
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Hello,
I am doing some analyses using TCGA data and noticed that the recommendation is to download the pre-calculated xCell data. However, I noticed that this data does not include normal (NT) samp…
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Go to results view mutations tab, switch to another transcript, click "Columns" -> "Clinical", click any checkbox to add a new clinical column, then click "Reset columns", most clinical columns disapp…
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For analysis purposes, i would like to understand the meaning and abbreviations behind the codes in sample names. Apart from the 4 or 5 first parts that are based on the TCGA project coding, i could n…
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http://localhost:8082/study/summary?id=esca_tcga_pan_can_atlas_2018%2Cnsclc_public_genie_bpc
```
curl 'http://localhost:8082/api/column-store/sample-lists-counts/fetch' \
-H 'Accept: applicat…
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There are some vestigial endpoints for importing data from the TCGA that haven't worked since the hosting service changed. The endpoints and models associated with this should be removed.
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test.keepX = list (
nitrogen = c(1:5),
enzyme = c(1:4),
soil = c(1:3),
otu = c(seq(100, 700, 10))
)
t1 = proc.time()
…
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I have been using data from TCGA SpliceSeq, and would like to obtain the protein sequences associated with each of the splice events in the database, but this data does not appear downloadable (or I c…
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Hi, @Xiyue-Wang
In paper, we mentioned that "TCGA-RCC is a subset of TCGA for the classification of three subtypes of (TCGA-KICH), (TCGA-KIRC), and (TCGA-KIRP). There are a total of 884 FFPE WSIs…