Showing : metagenomics • reset
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baySeq issues and questions
bayseq metagenomics
9.6 years ago • updated 9.3 years ago lordbleys • 0
5
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5
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2.0k
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.7 years ago patrick.schordert ▴ 30
2
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8
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3.4k
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edgeR for metagenomic data
edger metagenomics
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by ▴ 70
0
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5
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1.8k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.1 years ago David ▴ 860
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2
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2.0k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.1 years ago David ▴ 860
4
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4
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3.3k
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edgeR and gene filtering
edger metagenomics gene abundance gene filtering
8.6 years ago jtremblay514 • 0
2
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3
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6.2k
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DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 7.5 years ago by 42k • written 7.5 years ago by • 0
1
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3
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1.9k
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Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.8 years ago lauren.czaplicki • 0
4
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11
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2.2k
views
DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 6.7 years ago by 42k • written 6.7 years ago by ▴ 10
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1
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1.8k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
0
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2
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4.5k
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Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.5 years ago by ★ 1.6k • written 9.5 years ago by ▴ 100
1
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1
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1.2k
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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 5.5 years ago by ★ 3.0k • written 5.5 years ago by • 0
0
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1
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1.1k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.8 years ago by 42k • written 3.8 years ago by • 0
17
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4
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Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.8 years ago by ▴ 210 • written 3.8 years ago by ▴ 10
0
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2
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772
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 14 days ago by • 0 • written 12 months ago by • 0
0
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1
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861
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
0
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1
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1.5k
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mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.2 years ago by ▴ 280 • written 10.2 years ago by ★ 13k
0
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1
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1.3k
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Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 8.6 years ago by 42k • written 8.6 years ago by • 0
3
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3
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1.2k
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Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 3.1 years ago by 42k • written 3.1 years ago by • 0
0
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1
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792
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FDR Correction
dada2 Metagenomics DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
1
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4
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799
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How do I design my DESEQ experiment?
DESeq2 Metagenomics
15 months ago Michael • 0
2
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2
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1.2k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 22 months ago by ★ 4.2k • written 22 months ago by • 0
3
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5
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2.5k
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DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 7.5 years ago by 42k • written 7.5 years ago by • 0
0
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0
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393
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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
9 months ago Mohamed ▴ 30
8
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0
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3.6k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.9 years ago Martin Morgan 25k
0
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0
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1.3k
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.1 years ago David ▴ 860
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0
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1.3k
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.3 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.3k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
6.3 years ago jol.espinoz ▴ 40
0
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0
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1.0k
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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
3.2 years ago jol.espinoz ▴ 40
0
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1
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2.2k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.9 years ago by ★ 1.1k • written 2.9 years ago by • 0
1
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0
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643
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Shotgun metagenomics data analysis
Metagenomics abundance
19 months ago YASIR ▴ 10
0
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1
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921
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
22 months ago Jenny Drnevich ★ 2.0k
0
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2
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582
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Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
written 5 months ago by ★ 1.1k
0
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0
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992
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
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0
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572
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
17 months ago cwarden45 • 0
35 results • Page 1 of 1
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Comment: Deseq2 by Ram ▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error by giulia.nicoletto.1 • 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design by SamGG ▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2 by ATpoint ★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage by Michael Love 42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
Votes
Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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