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Dear TCGAbiolinks team,
When analyze differential methylation with large data set (~400 cases), the system memory (128Gbyte) is fully exhausted and the os system work very slowly.
Would you like t…
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Hey TCGAbiolinks-Team,
I don´t know if it is a SummarizedExperiment Problem or a TCGAbiolinks problem, but I hope someone can help.
I have a little problem subsetting a SummarizedExperiment and addi…
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We've got the gene expression data from TCGA downloaded from GDC and in a format that is appropriate for students to use, but we need to figure out how to make data accessible to students. Options inc…
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Hello,
I'm using the TCGAanalyze_Normalization function for GC content normalization for all TCGA cancer types, working on data downloaded from GDC in 2021 (before the recent changes in GDC data re…
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i am working on TCGA database and want to prepare clinical data for analysis and normalization.i have data in csv format ,for TCGA biolinks preparation file can be in CEL format. so how can i prepare…
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Hi,
When I download legacy exon quantification from *TCGAbiolinks*, the resulting `SummarizedExperiment` I get has the `@rowRanges` contain `start`, `end`, and `chromosome`.
It would be great if…
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(note: [this was crossposted at BioStars](https://www.biostars.org/p/234435/))
I am retrieving and parsing some data from GDC using TCGAbiolinks:
```
library(TCGAbiolinks)
patientdownload
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Hello!
I tried to download mutation data for project TCGA-STAD, but it showed an error with duplicated elements and "cases" column was NULL.
Code shows as below.
> query project = "TCGA-S…
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Hi,
This repository looks very promising! I really like the idea of doing a `Make` to get all the TCGA data in a tidy format for `R`.
However, I realized that the XENAbrowser `datapages > GCD TCGA…
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Please, I would be very appreciative if I could get some guidance on why this function is not working. All the MMRF functions work instead of the the MMRFGDC prepare function once STAR - Count data is…