Bioconductor WGCNA

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WGCNA Theory Scale-Free Topology

updated 15 hours ago by Garrett • 0 • written 9.1 years ago by brohawndg ▴ 150

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BatchEffect RNASeqData WGCNA DESeq2

updated 2 days ago by Ashley • 0 • written 10 months ago by zxc741xb • 0

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WGCNA

written 12 months ago by mauricio.microbiol • 0

3 results • Page 1 of 1

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Answer: OrgDb for maize by James W. MacDonald 65k

``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…

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…

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A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

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