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After reading through the documentation, I'm a little unclear whether the input compendium should be normalized at all prior to input. I think it should be raw (number of reads mapped to a transcript …
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When creating a new config file for analysis of subsets of the samples, which of the file names do I need to change?
I have two example config files below, where one is using the full set of sample…
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These days, I tried to use the TCGAquery_recount2 function to download tumor and normal uterine samples, but failed. The codes are as follow.I wonder if there is the problem in the platform.
Looking …
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https://mp.weixin.qq.com/s/twrBE7bxNxI2kvpI4G9G8Q
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https://mp.weixin.qq.com/s/twrBE7bxNxI2kvpI4G9G8Q
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Dear there,
I got an error when used TCGAquery_recount2 from TCGAbiolinks. Here are the code and the error as below. I did some search for the error but did not figure out why and how to fix it ou…
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Hi there,
Do you have the bigwig files for recount available? I tried to manually stitch together what I thought the link format might be e.g.
http://duffel.rail.bio/recount/v2/SRP042161/mean_S…
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I just finished training my first VAE with sophie! I used 861 RNA seq samples of Pseudomonas aeruginosa strain PAO1 as my input compendium.
(side note, it only took about an hour, and this compute…
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https://mp.weixin.qq.com/s/IuFSyqIPVZ_VB8opFoISVA
ixxmu updated
2 years ago
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Hi,
I am encountering an error where I am unable to filter for a specific sample type (i.e. Primary Tumor) using data from TCGAquery_SampleTypes for certain TCGA projects (i.e. TCGA-BRCA) on recoun…