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Recent Replies
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
•
0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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Chris Dean
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390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
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2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
by
dsull
★
6.0k
TPM is irrelevant for miRNA-seq; CPM works fine.
TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python
by
Wayne
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2.0k
"I'm also unsure what qualifies as a lateral gene."
The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
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90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
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Qroid
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Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
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390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
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GenoMax
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Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
•
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Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
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GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
by
Tatyana
•
0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro
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andres.firrincieli
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1. Maribaculaceae is a family not a genus
2. Who said that ASV with the same taxonomic classification must have the same behaviour?
3. With…
Comment: Question regarding WGCNA
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andres.firrincieli
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the within-group variability is so small that these look like technical replicates rather than independent biological replicates
Answer: Gene ontology and homologs
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geneontologyhelp
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No. Homology is defined as shared common ancestry.
Two genes that take part in the same biological process may not have the same functio…
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