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
2
votes
3
replies
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
0
votes
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
8
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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
2
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8
replies
3.4k
views
edgeR for metagenomic data
edger metagenomics
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ▴ 70
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
1
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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
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
4
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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
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
5
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5
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2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.7 years ago patrick.schordert ▴ 30
0
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2
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2.0k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.0 years ago David ▴ 860
1
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3
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1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.8 years ago lauren.czaplicki • 0
0
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5
replies
1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.0 years ago David ▴ 860
1
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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
0
votes
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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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
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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
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0
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1.3k
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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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0
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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
2
votes
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
1
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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
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
0
votes
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
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
0
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981
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
votes
1
reply
914
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
848
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
1
vote
4
replies
788
views
How do I design my DESEQ experiment?
DESeq2 Metagenomics
14 months ago Michael • 0
0
votes
1
reply
787
views
FDR Correction
dada2 Metagenomics DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
0
votes
2
replies
748
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 2 days ago by • 0 • written 11 months ago by • 0
1
vote
0
replies
632
views
Shotgun metagenomics data analysis
Metagenomics abundance
18 months ago YASIR ▴ 10
0
votes
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
2
replies
557
views
Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
written 4 months ago by ★ 1.1k
0
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0
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383
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
35 results • Page 1 of 1
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Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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