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phyloseq
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
HULFRED
▴ 10
0
votes
1
reply
2.0k
views
Error with phyloseq R package with Conda install
software error
phyloseq
anaconda
written 7.5 years ago by
kpitz23
• 0
0
votes
1
reply
659
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 5 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
0
votes
6
replies
1.3k
views
convert default phylip to sequential phylip
phyloseq
Phylogenetics
updated 11 months ago by
yrkkhdesiserials
• 0 • written 2.6 years ago by
memy
• 0
0
votes
0
replies
349
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
8 months ago
Mohamed
▴ 30
5 results • Page
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it always helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR? Are you starting with…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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