Showing : Metagenomics • reset
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 7 months ago by • 0 • written 21 months ago by • 0
0
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2
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846
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics dada2 MicrobiomeData
8 months ago • updated 6 months ago abhisek001 • 0
0
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1
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1.1k
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Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
updated 7 months ago by • 0 • written 14 months ago by ★ 1.1k
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674
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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
18 months ago Mohamed ▴ 30
1
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4
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1.1k
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How do I design my DESEQ experiment?
DESeq2 Metagenomics
2.0 years ago Michael • 0
0
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0
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822
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
2.2 years ago cwarden45 • 0
1
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0
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878
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Shotgun metagenomics data analysis
Metagenomics abundance
2.3 years ago YASIR ▴ 10
2
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2
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1.8k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 2.6 years ago by ★ 4.7k • written 2.6 years ago by • 0
0
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1
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1.2k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.6 years ago Jenny Drnevich ★ 2.0k
0
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1
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1.1k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
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1
reply
2.7k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.7 years ago by ★ 1.1k • written 3.7 years ago by • 0
0
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0
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1.3k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.7 years ago GlycineMax • 0
0
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1
reply
989
views
FDR Correction
dada2 Metagenomics DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
3
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3
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1.5k
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Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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0
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1.3k
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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
4.0 years ago jol.espinoz ▴ 40
18
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4
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40k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 4.5 years ago by ▴ 220 • written 4.5 years ago by ▴ 10
0
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1
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1.5k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
1
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1
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1.5k
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna weighted correlation network analysis correlation matrix scale-free topology metagenomics
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by • 0
0
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0
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1.6k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
7.1 years ago jol.espinoz ▴ 40
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0
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1.5k
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
7.1 years ago Jenny Drnevich ★ 2.0k
1
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1
reply
2.1k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 10
4
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11
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2.5k
views
DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 10
1
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3
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2.3k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.5 years ago lauren.czaplicki • 0
0
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0
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1.5k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.9 years ago David ▴ 860
3
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5
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2.8k
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DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
2
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3
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6.7k
views
DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
0
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5
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2.2k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.8 years ago David ▴ 860
0
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2
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2.4k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.8 years ago David ▴ 860
4
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4
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3.7k
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edgeR and gene filtering
edger metagenomics gene abundance gene filtering
9.4 years ago jtremblay514 • 0
0
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1
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1.5k
views
Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
8
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0
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3.9k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.7 years ago Martin Morgan 25k
2
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8
replies
3.9k
views
edgeR for metagenomic data
edger metagenomics
updated 9.7 years ago by ▴ 280 • written 9.7 years ago by ▴ 70
1
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5
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3.2k
views
baySeq issues and questions
bayseq metagenomics
10.3 years ago • updated 10.1 years ago lordbleys • 0
0
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2
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5.0k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 10.3 years ago by ★ 1.6k • written 10.3 years ago by ▴ 100
5
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5
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2.3k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
10.5 years ago patrick.schordert ▴ 30
0
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1
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1.8k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 11.0 years ago by ▴ 280 • written 11.0 years ago by ★ 13k
36 results • Page 1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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