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metagenomics
•
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0
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replies
91
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
4 weeks ago
Mohamed
▴ 20
0
votes
1
reply
233
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 3 months ago by
abhisek001
• 0
1
vote
4
replies
423
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
6 months ago
Michael
• 0
0
votes
0
replies
299
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
0
votes
0
replies
366
views
Shotgun metagenomics data analysis
Metagenomics
abundance
10 months ago
YASIR
• 0
2
votes
2
replies
686
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 13 months ago by
ATpoint
★ 3.4k • written 13 months ago by
Muhammad
• 0
0
votes
1
reply
614
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
14 months ago • updated 13 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
540
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 17 months ago by
Michael Love
40k • written 17 months ago by
Aditya
• 0
0
votes
1
reply
1.7k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.2 years ago by
Levi Waldron
1.1k • written 2.2 years ago by
Saraswati
• 0
0
votes
0
replies
684
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.3 years ago
GlycineMax
• 0
0
votes
1
reply
555
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 2.3 years ago by
Michael Love
40k • written 2.3 years ago by
GlycineMax
• 0
3
votes
3
replies
889
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 2.4 years ago by
Michael Love
40k • written 2.4 years ago by
Tom
• 0
0
votes
0
replies
762
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
14
votes
4
replies
25k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 3.1 years ago by
Ram
▴ 180 • written 3.1 years ago by
c.e.chong
▴ 10
0
votes
1
reply
899
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.1 years ago by
Michael Love
40k • written 3.2 years ago by
dc
• 0
1
vote
1
reply
903
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
Peter Langfelder
★ 2.8k • written 4.8 years ago by
eneas_aguirre
• 0
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
1.0k
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
5.6 years ago
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.4k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 5.8 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 5.8 years ago by
lilianeconteville
▴ 10
4
votes
11
replies
1.9k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 6.1 years ago by
Michael Love
40k • written 6.1 years ago by
ghanbari.msc
▴ 10
1
vote
3
replies
1.6k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.1 years ago
lauren.czaplicki
• 0
0
votes
0
replies
1.1k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
6.4 years ago
David
▴ 860
3
votes
5
replies
2.2k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 6.8 years ago by
Michael Love
40k • written 6.8 years ago by
Earendil
• 0
2
votes
3
replies
5.8k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 6.8 years ago by
Michael Love
40k • written 6.8 years ago by
pro_zac
• 0
0
votes
5
replies
1.5k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
7.4 years ago
David
▴ 860
0
votes
2
replies
1.7k
views
Advice on normalization with metagenomics data
metagenome
normalization
metagenomics
7.4 years ago
David
▴ 860
4
votes
4
replies
3.0k
views
edgeR and gene filtering
edger
metagenomics
gene abundance
gene filtering
7.9 years ago
jtremblay514
• 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
Michael Love
40k • written 8.0 years ago by
jessawbryant
• 0
8
votes
0
replies
3.3k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.2 years ago
Martin Morgan
25k
2
votes
8
replies
2.8k
views
edgeR for metagenomic data
edger
metagenomics
updated 8.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.3 years ago by
eleonoregravier
▴ 60
1
vote
5
replies
2.6k
views
baySeq issues and questions
bayseq
metagenomics
8.9 years ago • updated 8.7 years ago
lordbleys
• 0
0
votes
2
replies
4.1k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.9 years ago by
francesca.defilippis
▴ 100
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
0
votes
1
reply
1.3k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics
metagenomeSeq
Metagenomics
metagenomeSeq
updated 9.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.5 years ago by
Guest User
★ 12k
34 results • Page
1 of 1
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Replies
Comment: DMRcate design
by
James W. MacDonald
63k
That's what identical context means.
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?
Comment: Steps needed to change design (relevel factors) in DESeq2
by
jd774
• 0
Thanks for the example code, would the `"condition_1_vs_2"` and `"condition_2_vs_1"` giving same or different results on DEGs and normalize…
Answer: heatmap.2 - change column & row locations; angle / rotate
by
nehagoyal6397
• 0
Window 10 are comes with the new updates [how to fix connections to wireless displays in windows 10](http://fixwindows10connections.com) ju…
Comment: filtering out lowly expressed genes by groups
by
James W. MacDonald
63k
You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…
Votes
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
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