Showing : metagenomics • reset
0
votes
3
replies
973
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 12 days ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
165
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics dada2 MicrobiomeData
updated 15 days ago by • 0 • written 28 days ago by • 0
0
votes
2
replies
662
views
Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
written 7 months ago by ★ 1.1k
0
votes
0
replies
460
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
11 months ago Mohamed ▴ 30
1
vote
4
replies
878
views
How do I design my DESEQ experiment?
DESeq2 Metagenomics
17 months ago Michael • 0
0
votes
0
replies
632
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
19 months ago cwarden45 • 0
1
vote
0
replies
690
views
Shotgun metagenomics data analysis
Metagenomics abundance
21 months ago YASIR ▴ 10
2
votes
2
replies
1.4k
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 23 months ago by ★ 4.2k • written 24 months ago by • 0
0
votes
1
reply
996
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.0 years ago • updated 24 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
922
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
1
reply
2.4k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 3.1 years ago by ★ 1.1k • written 3.1 years ago by • 0
0
votes
0
replies
1.1k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.1 years ago GlycineMax • 0
0
votes
1
reply
843
views
FDR Correction
dada2 Metagenomics DESeq2
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
3
votes
3
replies
1.3k
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
0
votes
0
replies
1.1k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.4 years ago jol.espinoz ▴ 40
17
votes
4
replies
35k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.9 years ago by ▴ 210 • written 3.9 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 4.0 years ago by 42k • written 4.0 years ago by • 0
1
vote
1
reply
1.3k
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna weighted correlation network analysis correlation matrix scale-free topology metagenomics
updated 5.6 years ago by ★ 3.0k • written 5.6 years ago by • 0
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
6.5 years ago jol.espinoz ▴ 40
0
votes
0
replies
1.3k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.5 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
1.9k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.7 years ago by ▴ 280 • written 6.7 years ago by ▴ 10
4
votes
11
replies
2.3k
views
DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 10
1
vote
3
replies
2.0k
views
Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.9 years ago lauren.czaplicki • 0
0
votes
0
replies
1.4k
views
Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.3 years ago David ▴ 860
3
votes
5
replies
2.5k
views
DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 7.7 years ago by 42k • written 7.7 years ago by • 0
2
votes
3
replies
6.3k
views
DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 7.7 years ago by 42k • written 7.7 years ago by • 0
0
votes
5
replies
1.9k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.2 years ago David ▴ 860
0
votes
2
replies
2.1k
views
Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.2 years ago David ▴ 860
4
votes
4
replies
3.4k
views
edgeR and gene filtering
edger metagenomics gene abundance gene filtering
8.8 years ago jtremblay514 • 0
0
votes
1
reply
1.4k
views
Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 8.8 years ago by 42k • written 8.8 years ago by • 0
8
votes
0
replies
3.7k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.1 years ago Martin Morgan 25k
2
votes
8
replies
3.5k
views
edgeR for metagenomic data
edger metagenomics
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by ▴ 70
1
vote
5
replies
3.0k
views
baySeq issues and questions
bayseq metagenomics
9.7 years ago • updated 9.5 years ago lordbleys • 0
0
votes
2
replies
4.6k
views
Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.7 years ago by ★ 1.6k • written 9.7 years ago by ▴ 100
5
votes
5
replies
2.1k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.9 years ago patrick.schordert ▴ 30
0
votes
1
reply
1.6k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.4 years ago by ▴ 280 • written 10.4 years ago by ★ 13k
36 results • Page 1 of 1
Recent ...
Replies
Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 730
Popular Question to maltethodberg ▴ 180
Scholar to Michael Love 42k
Popular Question to Leonardo Collado Torres ★ 1.1k
Scholar to Gordon Smyth 51k
Locations • All
United States, just now
United States, 1 minute ago
WEHI, Melbourne, Australia, 10 minutes ago
France, 16 minutes ago
Slovakia, 23 minutes ago
Traffic: 489 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