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It turns out that our default RNA-seq pipeline happily analyzed IonTorrent or ABI data and produces seemingly reasonable data
[GSE67124](https://gemma.msl.ubc.ca/expressionExperiment/showExpression…
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RNA-Sequencing (RNA-Seq) is a popular method for determining the presence and quantity of RNA in biological samples. In this 3 hour workshop, we will use R to explore publicly-available RNA-Seq data f…
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Hi,
I am processing an scRNA-seq dataset containing 14 samples. For each sample, I performed the standard QC filtering based on nFeatures and mitochondrial gene percentage, followed by the identifi…
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Hi,
I am trying MOFA for integrating Proteomics and RNA-seq dataset. I run the following codes.
```
`dd_WO_batch
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Before this change https://github.com/samtools/htslib/pull/1854 U was changed to N when read by samtools
Now it will be changed to T
However, I think it would be "better" if we could preserve U …
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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 trying to import `mbn_sfu_2023` into a private installation of cbioportal and getting this error
```
ERROR: data_RNA_Seq_v2_mRNA_median_Zscores.txt: lines [1601, 1998, 2191, (17381 more)]: No…
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Hi,
I am afraid http://www.bioconductor.org/biocLite.R does not exist any more, does anyone know how to get around this?
Thanks in advance for your help.
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We would like to propose a continuation of the issue [448](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/448).
#### What are the scientific goals of the analysis?
Batch effects are c…
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Hi,
Any idea what does this error mean?
`visiumHD_object