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 18 months ago by • 0
0
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2
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722
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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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966
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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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607
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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
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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
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0
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755
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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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810
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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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1.7k
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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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1.0k
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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
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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
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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
920
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
3.7 years ago jol.espinoz ▴ 40
18
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4
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38k
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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
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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
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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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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
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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
7.3 years ago lauren.czaplicki • 0
0
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0
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1.5k
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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 8.0 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 8.1 years ago by 43k • written 8.1 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
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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
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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
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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
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baySeq issues and questions
bayseq metagenomics
10.1 years ago • updated 9.9 years ago lordbleys • 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
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
10.2 years ago patrick.schordert ▴ 30
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1
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1.7k
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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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Answer: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…
Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Maria please read the mirTarRnaSeq paper. In particular, Supplemental Table 2, clarifies all the statistical models, inputs and outputs. If…
Comment: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k
Telling me you can't do something without showing what you tried is not helpful. When posting here, try to put yourself in the shoes of peo…
Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Answer: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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