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Showing :
metagenomics
•
reset
1
vote
5
replies
2.1k
views
baySeq issues and questions
bayseq
metagenomics
7.6 years ago • updated 7.4 years ago
lordbleys
• 0
5
votes
5
replies
1.4k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
7.8 years ago
patrick.schordert
▴ 30
0
votes
5
replies
1.1k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
6.1 years ago
David
▴ 860
2
votes
8
replies
2.2k
views
edgeR for metagenomic data
edger
metagenomics
updated 7.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.0 years ago by
eleonoregravier
▴ 60
2
votes
3
replies
5.2k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 5.6 years ago by
Michael Love
37k • written 5.6 years ago by
pro_zac
• 0
4
votes
4
replies
2.5k
views
edgeR and gene filtering
edger
metagenomics
gene abundance
gene filtering
6.7 years ago
jtremblay514
• 0
0
votes
2
replies
1.3k
views
Advice on normalization with metagenomics data
metagenome
normalization
metagenomics
6.1 years ago
David
▴ 860
1
vote
3
replies
1.2k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
4.9 years ago
lauren.czaplicki
• 0
4
votes
11
replies
1.3k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 4.8 years ago by
Michael Love
37k • written 4.8 years ago by
ghanbari.msc
▴ 10
1
vote
1
reply
956
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 4.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 4.6 years ago by
lilianeconteville
▴ 10
0
votes
2
replies
3.6k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 7.6 years ago by
Luo Weijun
★ 1.5k • written 7.6 years ago by
francesca.defilippis
▴ 80
1
vote
1
reply
534
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna
weighted correlation network analysis
correlation matrix
scale-free topology
metagenomics
updated 3.5 years ago by
Peter Langfelder
★ 2.7k • written 3.5 years ago by
eneas_aguirre
• 0
11
votes
4
replies
12k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 22 months ago by
Ram
▴ 150 • written 22 months ago by
c.e.chong
▴ 10
0
votes
1
reply
558
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 23 months ago by
Michael Love
37k • written 23 months ago by
dc
• 0
0
votes
1
reply
1.0k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics
metagenomeSeq
Metagenomics
metagenomeSeq
updated 8.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.3 years ago by
Guest User
★ 12k
0
votes
1
reply
117
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 11 weeks ago by
Michael Love
37k • written 11 weeks ago by
Aditya
• 0
0
votes
1
reply
770
views
Influence of average genome size on DESeq2 results
deseq2
normalization
metagenomics
updated 6.7 years ago by
Michael Love
37k • written 6.7 years ago by
jessawbryant
• 0
3
votes
3
replies
367
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 14 months ago by
Michael Love
37k • written 14 months ago by
Tom
• 0
0
votes
1
reply
228
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 13 months ago by
Michael Love
37k • written 13 months ago by
GlycineMax
• 0
3
votes
5
replies
1.6k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 5.6 years ago by
Michael Love
37k • written 5.6 years ago by
Earendil
• 0
0
votes
0
replies
288
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
12 months ago
GlycineMax
• 0
8
votes
0
replies
2.8k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
7.0 years ago
Martin Morgan
25k
0
votes
0
replies
770
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
5.2 years ago
David
▴ 860
0
votes
0
replies
700
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
4.4 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
636
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna
transcriptome
big data
metagenomics
gene expression
4.4 years ago
jol.espinoz
▴ 40
0
votes
0
replies
323
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
15 months ago
jol.espinoz
▴ 40
0
votes
1
reply
747
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 12 months ago by
Levi Waldron
1.1k • written 12 months ago by
Saraswati
• 0
27 results • Page
1 of 1
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Replies
Comment: cellCounts() function floating point error
by
Yang Liao
▴ 340
Thanks for the report but the error cannot be reproduced. We tested `Rsubread` 2.10.3 in `R` 4.2.0 and `Bioconductor` 3.15, and `cellCounts…
Comment: rtracklayer export GRangesList as gtf and change attributes
by
James
• 0
I have found a way to export a GTF so that the 3rd column no longer lists **sequence_feature** but instead lists the feature, such as **exo…
Comment: Using Age or other numerical variable to model expression in deseq2
by
swbarnes2
★ 1.1k
You can import age and not make it a factor.
Comment: Using Age or other numerical variable to model expression in deseq2
by
krushnach80
• 0
"Why is that" no as an example i was citing that.."certainly don't want to make the interaction between the nuisance variable and your vari…
Comment: Using Age or other numerical variable to model expression in deseq2
by
James W. MacDonald
60k
You have to use age from that post? Why is that? It is rarely optimal to categorize age rather than use as a continuous variable. It takes …
Votes
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
Answer: Trouble importing my own Gene Ontology Annotation into topGO
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