Showing : Metagenomics • reset
17
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4
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33k
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Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.7 years ago by ▴ 210 • written 3.7 years ago by ▴ 10
8
votes
0
replies
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
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.7 years ago patrick.schordert ▴ 30
4
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4
replies
3.3k
views
edgeR and gene filtering
edger metagenomics gene abundance gene filtering
8.6 years ago jtremblay514 • 0
4
votes
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
3
votes
3
replies
1.2k
views
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
3
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5
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2.5k
views
DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 7.5 years ago by 42k • written 7.5 years ago by • 0
2
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2
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1.2k
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
2
votes
3
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6.2k
views
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
2
votes
8
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3.4k
views
edgeR for metagenomic data
edger metagenomics
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ▴ 70
1
vote
4
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790
views
How do I design my DESEQ experiment?
DESeq2 Metagenomics
14 months ago Michael • 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.8 years ago lauren.czaplicki • 0
1
vote
1
reply
1.2k
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna weighted correlation network analysis correlation matrix scale-free topology metagenomics
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by • 0
1
vote
1
reply
1.8k
views
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
1
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0
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634
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Shotgun metagenomics data analysis
Metagenomics abundance
18 months ago YASIR ▴ 10
1
vote
5
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2.9k
views
baySeq issues and questions
bayseq metagenomics
9.5 years ago • updated 9.3 years ago lordbleys • 0
0
votes
2
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562
views
Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
written 5 months ago by ★ 1.1k
0
votes
0
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982
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
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0
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566
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
0
votes
0
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385
views
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
0
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1
reply
1.5k
views
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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2
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4.5k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.5 years ago by ★ 1.6k • written 9.5 years ago by ▴ 100
0
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1
reply
1.3k
views
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
0
votes
2
replies
2.0k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.0 years ago David ▴ 860
0
votes
5
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1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.0 years ago David ▴ 860
0
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0
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1.3k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.1 years ago David ▴ 860
0
votes
0
replies
1.3k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.3 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.3k
views
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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1
reply
1.1k
views
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
0
votes
2
replies
754
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 5 days ago by • 0 • written 11 months ago by • 0
0
votes
0
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1.0k
views
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
votes
1
reply
851
views
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
votes
1
reply
2.2k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.9 years ago by ★ 1.1k • written 2.9 years ago by • 0
0
votes
1
reply
915
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
22 months ago • updated 21 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
788
views
FDR Correction
dada2 Metagenomics DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
35 results • Page 1 of 1
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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