Showing : metagenomics • reset
4
votes
11
replies
2.2k
views
DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 10
2
votes
8
replies
3.3k
views
edgeR for metagenomic data
edger metagenomics
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by ▴ 70
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.6 years ago patrick.schordert ▴ 30
3
votes
5
replies
2.4k
views
DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
0
votes
5
replies
1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
7.9 years ago David ▴ 860
1
vote
5
replies
2.9k
views
baySeq issues and questions
bayseq metagenomics
9.4 years ago • updated 9.2 years ago lordbleys • 0
1
vote
4
replies
736
views
How do I design my DESEQ experiment?
DESeq2 Metagenomics
13 months ago Michael • 0
15
votes
4
replies
32k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.7 years ago by ▴ 190 • written 3.7 years ago by ▴ 10
4
votes
4
replies
3.3k
views
edgeR and gene filtering
edger metagenomics gene abundance gene filtering
8.5 years ago jtremblay514 • 0
2
votes
3
replies
6.1k
views
DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.7 years ago lauren.czaplicki • 0
3
votes
3
replies
1.2k
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
2
votes
2
replies
1.2k
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
0
votes
2
replies
1.9k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.0 years ago David ▴ 860
0
votes
2
replies
500
views
Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
written 4 months ago by ★ 1.1k
0
votes
1
reply
1.3k
views
Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 8.5 years ago by 41k • written 8.5 years ago by • 0
0
votes
1
reply
759
views
FDR Correction
dada2 Metagenomics DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.4 years ago by ▴ 280 • written 6.4 years ago by ▴ 10
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 5.3 years ago by ★ 3.0k • written 5.3 years ago by • 0
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
votes
1
reply
671
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 7 days ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
1.5k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
0
votes
1
reply
806
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
votes
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by • 0
0
votes
1
reply
893
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
352
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
8 months ago Mohamed ▴ 30
8
votes
0
replies
3.6k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.8 years ago Martin Morgan 25k
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.0 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
6.2 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
6.2 years ago jol.espinoz ▴ 40
0
votes
0
replies
978
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.1 years ago jol.espinoz ▴ 40
1
vote
0
replies
604
views
Shotgun metagenomics data analysis
Metagenomics abundance
17 months ago YASIR ▴ 10
0
votes
0
replies
943
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
votes
0
replies
533
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
16 months ago cwarden45 • 0
35 results • Page 1 of 1
Recent ...
Replies
Answer: Why p value inconsistent when using different number of pathway score? by ATpoint ★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
Awards • All
Scholar to Robert Castelo ★ 3.2k
Popular Question to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Locations • All
France, 8 minutes ago
Vietnam, 18 minutes ago
UPF, Barcelona, Spain, 18 minutes ago
United States, 45 minutes ago
Estonia, 52 minutes ago
Traffic: 403 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6