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Hi @GeorgeBatch, while running the command bash `./0-download-LUSC-and-LUAD.sh`, I encountered an issue where the WSI used for testing in DSMIL are not being downloaded. According to the documentation…
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I am using TCGA-LGG data. I used the following code but getting blank output.
I have saved genes and probesets under genes and probesets.
`MCPcounter.estimate(rna, featuresType = "ENSEMBL_ID",
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Hi and thanks for this very useful package.
I've been testing it on some internal datasets using both WES and targeted data. I've had an issue with the targeted data which I'd like to report (very …
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Hi RMolania! Thanks for the very useful approach. I want to use RUV-III with PRPS for non-TCGA RNA-seq data, but I don't know how to process the non-TCGA RNA-seq data to use RUV-III with PRPS. Would y…
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i am using this issue to provide info on the data i use when benchmarking wsinfer in qupath.
image: TCGA-3C-AALI-01Z-00-DX1.F6E9A5DF-D8FB-45CF-B4BD-C6B76294C291.svs ([link to image for download](ht…
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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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GDCdownload(query_col_wxs, directory = "TCGA_DATA_DL")
Downloading data for project TCGA-COAD
GDCdownload will download 457 files. A total of 82.8324 MB
Downloading as: Sat_Feb_17_21_15_58_2024.tar…
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https://shixiangwang.github.io/home/en/post/ucscxenatools-201908/
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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…