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Metagenomics
•
reset
0
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replies
68
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
5 weeks ago
cwarden45
• 0
0
votes
0
replies
97
views
Shotgun metagenomics data analysis
Metagenomics
abundance
12 weeks ago
YASIR
• 0
2
votes
2
replies
328
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 5 months ago by
ATpoint
★ 2.1k • written 5 months ago by
Muhammad
• 0
0
votes
1
reply
275
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
6 months ago • updated 5 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
281
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 9 months ago by
Michael Love
39k • written 9 months ago by
Aditya
• 0
0
votes
1
reply
1.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 19 months ago by
Levi Waldron
1.1k • written 19 months ago by
Saraswati
• 0
0
votes
0
replies
439
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
19 months ago
GlycineMax
• 0
0
votes
1
reply
361
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 20 months ago by
Michael Love
39k • written 20 months ago by
GlycineMax
• 0
3
votes
3
replies
551
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 21 months ago by
Michael Love
39k • written 21 months ago by
Tom
• 0
0
votes
0
replies
479
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
22 months ago
jol.espinoz
▴ 40
12
votes
4
replies
18k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 2.4 years ago by
Ram
▴ 160 • written 2.4 years ago by
c.e.chong
▴ 10
0
votes
1
reply
694
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 2.5 years ago by
Michael Love
39k • written 2.5 years ago by
dc
• 0
1
vote
1
reply
666
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna
weighted correlation network analysis
correlation matrix
scale-free topology
metagenomics
updated 4.1 years ago by
Peter Langfelder
★ 2.7k • written 4.1 years ago by
eneas_aguirre
• 0
0
votes
0
replies
750
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna
transcriptome
big data
metagenomics
gene expression
5.0 years ago
jol.espinoz
▴ 40
0
votes
0
replies
809
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
5.0 years ago
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.1k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 5.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 5.2 years ago by
lilianeconteville
▴ 10
4
votes
11
replies
1.5k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 5.4 years ago by
Michael Love
39k • written 5.4 years ago by
ghanbari.msc
▴ 10
1
vote
3
replies
1.4k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
5.4 years ago
lauren.czaplicki
• 0
0
votes
0
replies
908
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
5.8 years ago
David
▴ 860
3
votes
5
replies
1.9k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 6.2 years ago by
Michael Love
39k • written 6.2 years ago by
Earendil
• 0
2
votes
3
replies
5.4k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 6.2 years ago by
Michael Love
39k • written 6.2 years ago by
pro_zac
• 0
0
votes
5
replies
1.3k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
6.7 years ago
David
▴ 860
0
votes
2
replies
1.4k
views
Advice on normalization with metagenomics data
metagenome
normalization
metagenomics
6.7 years ago
David
▴ 860
4
votes
4
replies
2.7k
views
edgeR and gene filtering
edger
metagenomics
gene abundance
gene filtering
7.3 years ago
jtremblay514
• 0
0
votes
1
reply
878
views
Influence of average genome size on DESeq2 results
deseq2
normalization
metagenomics
updated 7.3 years ago by
Michael Love
39k • written 7.3 years ago by
jessawbryant
• 0
8
votes
0
replies
3.0k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
7.6 years ago
Martin Morgan
25k
2
votes
8
replies
2.4k
views
edgeR for metagenomic data
edger
metagenomics
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
eleonoregravier
▴ 60
1
vote
5
replies
2.3k
views
baySeq issues and questions
bayseq
metagenomics
8.2 years ago • updated 8.0 years ago
lordbleys
• 0
0
votes
2
replies
3.8k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 8.2 years ago by
Luo Weijun
★ 1.6k • written 8.2 years ago by
francesca.defilippis
▴ 80
5
votes
5
replies
1.5k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
8.4 years ago
patrick.schordert
▴ 30
0
votes
1
reply
1.1k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics
metagenomeSeq
Metagenomics
metagenomeSeq
updated 8.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.9 years ago by
Guest User
★ 12k
31 results • Page
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
on which data type limma::removeBatchEffect can be applyed?
How can I draw a barplot of complexheatmap according 'Tumor Type'
on which data type limma::removeBatchEffect can be applyed?
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
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