Showing : metagenomics • reset
4
votes
11
replies
1.9k
views
DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 6.1 years ago by 40k • written 6.1 years ago by ▴ 10
2
votes
8
replies
2.8k
views
edgeR for metagenomic data
edger metagenomics
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by ▴ 70
0
votes
5
replies
1.6k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
7.4 years ago David ▴ 860
3
votes
5
replies
2.2k
views
DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 6.8 years ago by 40k • written 6.8 years ago by • 0
1
vote
5
replies
2.6k
views
baySeq issues and questions
bayseq metagenomics
8.9 years ago • updated 8.7 years ago lordbleys • 0
5
votes
5
replies
1.8k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.0 years ago patrick.schordert ▴ 30
1
vote
4
replies
446
views
How do I design my DESEQ experiment?
DESeq2 Metagenomics
7 months ago Michael • 0
4
votes
4
replies
3.0k
views
edgeR and gene filtering
edger metagenomics gene abundance gene filtering
8.0 years ago jtremblay514 • 0
14
votes
4
replies
26k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.1 years ago by ▴ 180 • written 3.1 years ago by ▴ 10
1
vote
3
replies
1.6k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.1 years ago lauren.czaplicki • 0
3
votes
3
replies
906
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 2.5 years ago by 40k • written 2.5 years ago by • 0
2
votes
3
replies
5.8k
views
DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 6.9 years ago by 40k • written 6.9 years ago by • 0
0
votes
2
replies
1.7k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
7.4 years ago David ▴ 860
2
votes
2
replies
709
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 14 months ago by ★ 3.4k • written 14 months ago by • 0
0
votes
2
replies
4.1k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 8.9 years ago by ★ 1.6k • written 8.9 years ago by ▴ 100
0
votes
1
reply
1.7k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.3 years ago by 1.1k • written 2.3 years ago by • 0
0
votes
1
reply
628
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
14 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
569
views
FDR Correction
dada2 Metagenomics DESeq2
updated 2.4 years ago by 40k • written 2.4 years ago by • 0
1
vote
1
reply
1.4k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 5.9 years ago by ▴ 280 • written 5.9 years ago by ▴ 10
1
vote
1
reply
919
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna weighted correlation network analysis correlation matrix scale-free topology metagenomics
updated 4.8 years ago by ★ 2.8k • written 4.8 years ago by • 0
0
votes
1
reply
912
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
0
votes
1
reply
249
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
written 4 months ago by • 0
0
votes
1
reply
1.3k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 9.6 years ago by ▴ 280 • written 9.6 years ago by ★ 12k
0
votes
1
reply
558
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 18 months ago by 40k • written 18 months ago by • 0
0
votes
1
reply
1.1k
views
Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 8.0 years ago by 40k • written 8.0 years ago by • 0
0
votes
0
replies
106
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
6 weeks ago Mohamed ▴ 20
8
votes
0
replies
3.3k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.3 years ago Martin Morgan 25k
0
votes
0
replies
1.1k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
6.5 years ago David ▴ 860
0
votes
0
replies
1.1k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
5.6 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.0k
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
5.6 years ago jol.espinoz ▴ 40
0
votes
0
replies
780
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
2.5 years ago jol.espinoz ▴ 40
0
votes
0
replies
376
views
Shotgun metagenomics data analysis
Metagenomics abundance
11 months ago YASIR • 0
0
votes
0
replies
697
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.3 years ago GlycineMax • 0
0
votes
0
replies
308
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
9 months ago cwarden45 • 0
34 results • Page 1 of 1
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Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Answer: Error MakeOrgPackagefromNCBI
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
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