Showing : Metagenomics • reset
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 5 months ago by • 0 • written 19 months ago by • 0
0
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2
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747
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics dada2 MicrobiomeData
6 months ago • updated 4 months ago abhisek001 • 0
0
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1
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981
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Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
updated 5 months ago by • 0 • written 12 months ago by ★ 1.1k
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617
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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
16 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
22 months ago Michael • 0
0
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0
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762
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
2.0 years ago cwarden45 • 0
1
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0
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819
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Shotgun metagenomics data analysis
Metagenomics abundance
2.2 years ago YASIR ▴ 10
2
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2
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1.7k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 2.4 years ago by ★ 4.6k • written 2.4 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 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 2.7 years ago by 43k • written 2.7 years ago by • 0
0
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1
reply
2.6k
views
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
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.5 years ago GlycineMax • 0
0
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1
reply
935
views
FDR Correction
dada2 Metagenomics DESeq2
updated 3.6 years ago by 43k • written 3.6 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
3.8 years ago jol.espinoz ▴ 40
18
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4
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39k
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Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 4.4 years ago by ▴ 220 • written 4.4 years ago by ▴ 10
0
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1
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1.4k
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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
views
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
6.9 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
6.9 years ago Jenny Drnevich ★ 2.0k
1
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1
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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
7.4 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
7.7 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 8.1 years ago by 43k • written 8.1 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 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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5
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2.1k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.6 years ago David ▴ 860
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2
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2.3k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.7 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
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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
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Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.5 years ago Martin Morgan 25k
2
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8
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3.8k
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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3.2k
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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4.9k
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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
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2.2k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
10.3 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: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0
After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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