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Metagenomics
•
reset
1
vote
5
replies
2.9k
views
baySeq issues and questions
bayseq
metagenomics
9.5 years ago • updated 9.3 years ago
lordbleys
• 0
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
9.7 years ago
patrick.schordert
▴ 30
2
votes
8
replies
3.4k
views
edgeR for metagenomic data
edger
metagenomics
updated 8.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.9 years ago by
eleonoregravier
▴ 70
0
votes
5
replies
1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
8.0 years ago
David
▴ 860
0
votes
2
replies
2.0k
views
Advice on normalization with metagenomics data
metagenome
normalization
metagenomics
8.0 years ago
David
▴ 860
4
votes
4
replies
3.3k
views
edgeR and gene filtering
edger
metagenomics
gene abundance
gene filtering
8.6 years ago
jtremblay514
• 0
2
votes
3
replies
6.2k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 7.5 years ago by
Michael Love
42k • written 7.5 years ago by
pro_zac
• 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.8 years ago
lauren.czaplicki
• 0
4
votes
11
replies
2.2k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 6.7 years ago by
Michael Love
42k • written 6.7 years ago by
ghanbari.msc
▴ 10
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 6.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.5 years ago by
lilianeconteville
▴ 10
0
votes
2
replies
4.5k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 9.5 years ago by
Luo Weijun
★ 1.6k • written 9.5 years ago by
francesca.defilippis
▴ 100
1
vote
1
reply
1.2k
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna
weighted correlation network analysis
correlation matrix
scale-free topology
metagenomics
updated 5.4 years ago by
Peter Langfelder
★ 3.0k • written 5.4 years ago by
eneas_aguirre
• 0
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.8 years ago by
Michael Love
42k • written 3.8 years ago by
dc
• 0
17
votes
4
replies
33k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 3.7 years ago by
Ram
▴ 210 • written 3.7 years ago by
c.e.chong
▴ 10
0
votes
2
replies
746
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 1 day ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
1
reply
846
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
Aditya
• 0
0
votes
1
reply
1.5k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics
metagenomeSeq
Metagenomics
metagenomeSeq
updated 10.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 10.2 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
Influence of average genome size on DESeq2 results
deseq2
normalization
metagenomics
updated 8.6 years ago by
Michael Love
42k • written 8.6 years ago by
jessawbryant
• 0
3
votes
3
replies
1.2k
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 3.1 years ago by
Michael Love
42k • written 3.1 years ago by
Tom
• 0
0
votes
1
reply
785
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 3.0 years ago by
Michael Love
42k • written 3.0 years ago by
GlycineMax
• 0
1
vote
4
replies
786
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
14 months ago
Michael
• 0
2
votes
2
replies
1.2k
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 21 months ago by
ATpoint
★ 4.1k • written 21 months ago by
Muhammad
• 0
3
votes
5
replies
2.5k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 7.5 years ago by
Michael Love
42k • written 7.5 years ago by
Earendil
• 0
0
votes
0
replies
381
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
9 months ago
Mohamed
▴ 30
8
votes
0
replies
3.6k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.9 years ago
Martin Morgan
25k
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
7.1 years ago
David
▴ 860
0
votes
0
replies
1.3k
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
6.3 years ago
Jenny Drnevich
★ 2.0k
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
6.3 years ago
jol.espinoz
▴ 40
0
votes
0
replies
1.0k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.2 years ago
jol.espinoz
▴ 40
0
votes
1
reply
2.2k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.9 years ago by
Levi Waldron
★ 1.1k • written 2.9 years ago by
Saraswati
• 0
1
vote
0
replies
631
views
Shotgun metagenomics data analysis
Metagenomics
abundance
18 months ago
YASIR
▴ 10
0
votes
1
reply
913
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
22 months ago • updated 21 months ago
Jenny Drnevich
★ 2.0k
0
votes
2
replies
554
views
Job:
Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics
curatedMetagenomicData
bugsigdbr
written 4 months ago by
Levi Waldron
★ 1.1k
0
votes
0
replies
977
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.9 years ago
GlycineMax
• 0
0
votes
0
replies
565
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
17 months ago
cwarden45
• 0
35 results • Page
1 of 1
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Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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