Showing : Metagenomics • reset
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
5 weeks ago cwarden45 • 0
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Shotgun metagenomics data analysis
Metagenomics abundance
12 weeks ago YASIR • 0
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2
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 5 months ago by ★ 2.1k • written 5 months ago by • 0
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
6 months ago • updated 5 months ago Jenny Drnevich ★ 2.0k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 9 months ago by 39k • written 9 months ago by • 0
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1.1k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 19 months ago by 1.1k • written 19 months ago by • 0
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439
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
19 months ago GlycineMax • 0
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361
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FDR Correction
dada2 Metagenomics DESeq2
updated 20 months ago by 39k • written 20 months ago by • 0
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551
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Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 21 months ago by 39k • written 21 months ago by • 0
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479
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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
22 months ago jol.espinoz ▴ 40
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Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 2.4 years ago by ▴ 160 • written 2.4 years ago by ▴ 10
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694
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 2.5 years ago by 39k • written 2.5 years ago by • 0
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666
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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 4.1 years ago by ★ 2.7k • written 4.1 years ago by • 0
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
5.0 years ago jol.espinoz ▴ 40
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
5.0 years ago Jenny Drnevich ★ 2.0k
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1
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1.1k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by ▴ 10
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11
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1.5k
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DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 5.4 years ago by 39k • written 5.4 years ago by ▴ 10
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3
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1.4k
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Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
5.4 years ago lauren.czaplicki • 0
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
5.8 years ago David ▴ 860
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5
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1.9k
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DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 6.2 years ago by 39k • written 6.2 years ago by • 0
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5.4k
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DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 6.2 years ago by 39k • written 6.2 years ago by • 0
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5
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1.3k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
6.7 years ago David ▴ 860
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1.4k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
6.7 years ago David ▴ 860
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4
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2.7k
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edgeR and gene filtering
edger metagenomics gene abundance gene filtering
7.3 years ago jtremblay514 • 0
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878
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Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 7.3 years ago by 39k • written 7.3 years ago by • 0
8
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3.0k
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Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
7.6 years ago Martin Morgan 25k
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8
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2.4k
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edgeR for metagenomic data
edger metagenomics
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 60
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2.3k
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baySeq issues and questions
bayseq metagenomics
8.2 years ago • updated 8.0 years ago lordbleys • 0
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3.8k
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Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 8.2 years ago by ★ 1.6k • written 8.2 years ago by ▴ 80
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
8.4 years ago patrick.schordert ▴ 30
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mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ★ 12k
31 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
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on which data type limma::removeBatchEffect can be applyed?
How can I draw a barplot of complexheatmap according 'Tumor Type'
on which data type limma::removeBatchEffect can be applyed?
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
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