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Showing :
metagenomics
•
reset
1
vote
5
replies
2.2k
views
baySeq issues and questions
bayseq
metagenomics
7.8 years ago • updated 7.6 years ago
lordbleys
• 0
5
votes
5
replies
1.4k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
7.9 years ago
patrick.schordert
▴ 30
2
votes
8
replies
2.2k
views
edgeR for metagenomic data
edger
metagenomics
updated 7.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.2 years ago by
eleonoregravier
▴ 60
0
votes
5
replies
1.1k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
6.3 years ago
David
▴ 860
2
votes
3
replies
5.3k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 5.7 years ago by
Michael Love
37k • written 5.7 years ago by
pro_zac
• 0
0
votes
2
replies
1.3k
views
Advice on normalization with metagenomics data
metagenome
normalization
metagenomics
6.3 years ago
David
▴ 860
4
votes
4
replies
2.5k
views
edgeR and gene filtering
edger
metagenomics
gene abundance
gene filtering
6.9 years ago
jtremblay514
• 0
0
votes
2
replies
117
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 12 days ago by
ATpoint
★ 1.4k • written 13 days ago by
Muhammad
• 0
0
votes
1
reply
1.1k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics
metagenomeSeq
Metagenomics
metagenomeSeq
updated 8.4 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.4 years ago by
Guest User
★ 12k
0
votes
2
replies
3.7k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 7.8 years ago by
Luo Weijun
★ 1.5k • written 7.8 years ago by
francesca.defilippis
▴ 80
0
votes
1
reply
798
views
Influence of average genome size on DESeq2 results
deseq2
normalization
metagenomics
updated 6.9 years ago by
Michael Love
37k • written 6.9 years ago by
jessawbryant
• 0
3
votes
5
replies
1.7k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 5.7 years ago by
Michael Love
37k • written 5.7 years ago by
Earendil
• 0
4
votes
11
replies
1.4k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 5.0 years ago by
Michael Love
37k • written 5.0 years ago by
ghanbari.msc
▴ 10
1
vote
1
reply
1.0k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 4.8 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 4.8 years ago by
lilianeconteville
▴ 10
1
vote
1
reply
564
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna
weighted correlation network analysis
correlation matrix
scale-free topology
metagenomics
updated 3.7 years ago by
Peter Langfelder
★ 2.7k • written 3.7 years ago by
eneas_aguirre
• 0
0
votes
1
reply
590
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 2.1 years ago by
Michael Love
37k • written 2.1 years ago by
dc
• 0
11
votes
4
replies
13k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 24 months ago by
Ram
▴ 150 • written 24 months ago by
c.e.chong
▴ 10
0
votes
1
reply
152
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 4 months ago by
Michael Love
37k • written 4 months ago by
Aditya
• 0
3
votes
3
replies
413
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 16 months ago by
Michael Love
37k • written 16 months ago by
Tom
• 0
0
votes
1
reply
258
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 14 months ago by
Michael Love
37k • written 15 months ago by
GlycineMax
• 0
1
vote
3
replies
1.2k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
5.0 years ago
lauren.czaplicki
• 0
0
votes
0
replies
797
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
5.3 years ago
David
▴ 860
0
votes
0
replies
724
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
4.5 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
313
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
14 months ago
GlycineMax
• 0
0
votes
0
replies
365
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
17 months ago
jol.espinoz
▴ 40
8
votes
0
replies
2.9k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
7.1 years ago
Martin Morgan
25k
0
votes
0
replies
664
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna
transcriptome
big data
metagenomics
gene expression
4.5 years ago
jol.espinoz
▴ 40
0
votes
1
reply
863
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 14 months ago by
Levi Waldron
1.1k • written 14 months ago by
Saraswati
• 0
0
votes
1
reply
115
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
28 days ago • updated 15 days ago
Jenny Drnevich
★ 2.0k
29 results • Page
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Answer: Design and contrast matrices for analyzing the effect of two factors of interest
by
Gordon Smyth
46k
> In a typical regression, I would just add them to the model when estimating my coefficients of interest Why not do the same with limma? …
Comment: TPM normalization starting with read counts
by
Gordon Smyth
46k
> So you think my method in TPM normalization that I introduced above is not good? Your computation of RPKM using edgeR is fine, provided …
Comment: error in package GenVisR while installing
by
堃
• 0
Package ‘FField’ was removed from the CRAN repository.[enter link description here][1] I installed FField by using remotes::install_github…
Comment: DESeq 2 failes to load
by
Ruggero
• 0
This solved the error, in case someone else is having compilation errors from installing RSQllite: install.packages('RSQLite', repos='http…
Comment: pathview says my nonmodel species is unknown: "species invalid"
by
Guido Hooiveld
★ 3.3k
A while ago a faced the same for another non-model organism. I was able to get it working using a 'hack'. This hack is nothing more than m…
Votes
DiffBind affinity vs occupancy Heatmaps
Answer: How to remove dendrogram from pheatmaps?
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: conceptual question about FDR, FDR adjusted p-value and q-value
A: How to select summit size for histone ChiP-Seq in Diffbind
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Gordon Smyth
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donnenfieldjonah
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Guido Hooiveld
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