Showing : Metagenomics • reset
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Species level information couldn't find with DADA2 bioconductor package
Metagenomics dada2 MicrobiomeData
written 20 months ago by • 0
0
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3
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2.0k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 19 months ago by • 0 • written 2.7 years ago by • 0
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1
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1.5k
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Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
updated 19 months ago by • 0 • written 2.2 years ago by ★ 1.1k
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968
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.5 years ago Mohamed ▴ 30
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4
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1.7k
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How do I design my DESEQ experiment?
DESeq2 Metagenomics
3.0 years ago Michael • 0
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0
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1.1k
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
3.2 years ago cwarden45 • 0
1
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0
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1.2k
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Shotgun metagenomics data analysis
Metagenomics abundance
3.3 years ago YASIR ▴ 10
2
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2
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2.5k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
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1
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1.5k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.6 years ago Jenny Drnevich ★ 2.0k
0
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1
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1.5k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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1
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3.2k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 4.7 years ago by ★ 1.1k • written 4.7 years ago by • 0
0
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0
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1.6k
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
4.7 years ago GlycineMax • 0
0
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1
reply
1.3k
views
FDR Correction
dada2 Metagenomics DESeq2
updated 4.7 years ago by 43k • written 4.8 years ago by • 0
3
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3
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1.9k
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Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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0
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1.7k
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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
4.9 years ago jol.espinoz ▴ 40
18
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4
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43k
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Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 5.5 years ago by ▴ 220 • written 5.5 years ago by ▴ 10
0
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1
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1.8k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
1
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1
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2.1k
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WGCNA threshold without prior knowledge of scale-free propery
wgcna weighted correlation network analysis correlation matrix scale-free topology metagenomics
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by • 0
0
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0
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1.9k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
8.0 years ago jol.espinoz ▴ 40
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0
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1.9k
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
8.0 years ago Jenny Drnevich ★ 2.0k
1
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1
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2.4k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by ▴ 10
4
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11
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3.1k
views
DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 10
1
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3
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2.7k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
8.5 years ago lauren.czaplicki • 0
0
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0
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1.8k
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
8.8 years ago David ▴ 860
3
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5
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3.1k
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DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
2
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3
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7.4k
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DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 9.2 years ago by 43k • written 9.3 years ago by • 0
0
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5
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2.6k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
9.8 years ago David ▴ 860
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2
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2.8k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
9.8 years ago David ▴ 860
4
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4
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4.4k
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edgeR and gene filtering
edger metagenomics gene abundance gene filtering
10.4 years ago jtremblay514 • 0
0
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1
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1.8k
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Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 10.4 years ago by 43k • written 10.4 years ago by • 0
8
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0
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4.3k
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Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
10.7 years ago Martin Morgan 25k
2
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8
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4.6k
views
edgeR for metagenomic data
edger metagenomics
updated 10.7 years ago by ▴ 280 • written 10.7 years ago by ▴ 70
1
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5
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3.6k
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baySeq issues and questions
bayseq metagenomics
11.3 years ago • updated 11.1 years ago lordbleys • 0
0
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2
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5.5k
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Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 11.3 years ago by ★ 1.6k • written 11.3 years ago by ▴ 100
5
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5
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2.7k
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
11.4 years ago patrick.schordert ▴ 30
0
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1
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2.0k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 12.0 years ago by ▴ 280 • written 12.0 years ago by ★ 13k
36 results • Page 1 of 1
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Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
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Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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