Showing : metagenomics • reset
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 4 months ago by • 0 • written 18 months ago by • 0
0
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2
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714
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Species level information couldn't find with DADA2 bioconductor package
Metagenomics dada2 MicrobiomeData
5 months ago • updated 3 months ago abhisek001 • 0
0
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1
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957
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Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
updated 4 months ago by • 0 • written 11 months ago by ★ 1.1k
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603
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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
15 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
21 months ago Michael • 0
0
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0
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748
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
24 months ago cwarden45 • 0
1
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0
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804
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Shotgun metagenomics data analysis
Metagenomics abundance
2.1 years ago YASIR ▴ 10
2
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2
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1.6k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 2.3 years ago by ★ 4.6k • written 2.3 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
2.4 years ago • updated 2.3 years ago Jenny Drnevich ★ 2.0k
0
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1
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1.0k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
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1
reply
2.6k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.5 years ago by ★ 1.1k • written 3.5 years ago by • 0
0
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0
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1.2k
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.5 years ago GlycineMax • 0
0
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1
reply
918
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FDR Correction
dada2 Metagenomics DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
3
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3
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1.4k
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Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 3.7 years ago by 43k • written 3.7 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
3.7 years ago jol.espinoz ▴ 40
18
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4
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38k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 4.3 years ago by ▴ 220 • written 4.3 years ago by ▴ 10
0
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1
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1.3k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
1
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1
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1.4k
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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 6.0 years ago by ★ 3.0k • written 6.0 years ago by • 0
0
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0
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1.5k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
6.8 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
6.8 years ago Jenny Drnevich ★ 2.0k
1
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1
reply
2.0k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.1 years ago by ▴ 280 • written 7.1 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 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
1
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3
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2.2k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
7.3 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
7.6 years ago David ▴ 860
3
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5
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2.7k
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DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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3
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6.6k
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DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
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5
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2.1k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.6 years ago David ▴ 860
0
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2
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2.3k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.6 years ago David ▴ 860
4
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4
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3.6k
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edgeR and gene filtering
edger metagenomics gene abundance gene filtering
9.2 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 9.2 years ago by 43k • written 9.2 years ago by • 0
8
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0
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3.8k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.4 years ago Martin Morgan 25k
2
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8
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3.7k
views
edgeR for metagenomic data
edger metagenomics
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by ▴ 70
1
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5
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3.1k
views
baySeq issues and questions
bayseq metagenomics
10.1 years ago • updated 9.9 years ago lordbleys • 0
0
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2
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4.8k
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Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 10.1 years ago by ★ 1.6k • written 10.1 years ago by ▴ 100
5
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5
replies
2.2k
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
10.2 years ago patrick.schordert ▴ 30
0
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1
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1.7k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.8 years ago by ▴ 280 • written 10.8 years ago by ★ 13k
36 results • Page 1 of 1
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Comment: Running multiple KNN queries in parallel by SamGG ▴ 360
Thank you for your detailed answer, I appreciate it and your work.
Answer: Running multiple KNN queries in parallel by Aaron Lun ★ 28k
That is correct - you can't pass the prebuilt objects to different processes. Maybe `MulticoreParam()` might work on POSIX systems but I'm …
Answer: RSubread output significantly different from bash Subread output by Gordon Smyth 52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square by Michael Love 43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Votes
Answer: Running multiple KNN queries in parallel
Answer: Running multiple KNN queries in parallel
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
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