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Species level information couldn't find with DADA2 bioconductor package
Metagenomics dada2 MicrobiomeData
7 months ago • updated 5 months ago abhisek001 • 0
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How to correctly interpret ALDEx2 output - differential abundance testing
MicrobiomeData ALDEx2
updated 22 months ago by • 0 • written 2.2 years ago by • 0
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Query regarding error in installation of "microbiomeutilities" R package
MicrobiomeData R microbiomeutilities Install
2.0 years ago abhisek001 • 0
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
2.2 years ago Levi Waldron ★ 1.1k
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HMP1-II Metagenomic Data
MicrobiomeData curatedMetagenomicData
2.2 years ago Pauline ▴ 20
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.4 years ago Julieta • 0
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
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Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
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Answer: WGCNA with paired samples by Ivo • 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
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Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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