Bioconductor Cibersort

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cibersort deconvR immune

updated 10 days ago by ivorychan7777 • 0 • written 14 months ago by 609b0d25 • 0

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normalization r vst cibersort

updated 3.7 years ago by Kevin Blighe ★ 3.9k • written 3.7 years ago by Matan G. ▴ 60

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Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0

Understood, Thank you very much for the reply, very kind.

Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k

"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k

These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…

Comment: DEG with low counts by Michael Love 41k

These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…

Comment: DESeq filtering specific to contrasts by Michael Love 41k

If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…

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A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

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