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Metagenomics
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Job:
Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics
curatedMetagenomicData
bugsigdbr
written 3 months ago by
Levi Waldron
★ 1.1k
0
votes
0
replies
329
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
7 months ago
Mohamed
▴ 30
0
votes
1
reply
560
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
1
vote
4
replies
705
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
13 months ago
Michael
• 0
0
votes
0
replies
493
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
15 months ago
cwarden45
• 0
1
vote
0
replies
576
views
Shotgun metagenomics data analysis
Metagenomics
abundance
17 months ago
YASIR
▴ 10
2
votes
2
replies
1.1k
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 19 months ago by
ATpoint
★ 4.0k • written 20 months ago by
Muhammad
• 0
0
votes
1
reply
871
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
20 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
769
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 24 months ago by
Michael Love
41k • written 24 months ago by
Aditya
• 0
0
votes
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.8 years ago by
Levi Waldron
★ 1.1k • written 2.8 years ago by
Saraswati
• 0
0
votes
0
replies
917
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
1
reply
733
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
GlycineMax
• 0
3
votes
3
replies
1.1k
views
Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics
DESeq2
Metatranscriptomics
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
Tom
• 0
0
votes
0
replies
950
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.0 years ago
jol.espinoz
▴ 40
15
votes
4
replies
31k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 3.6 years ago by
Ram
▴ 190 • written 3.6 years ago by
c.e.chong
▴ 10
0
votes
1
reply
1.1k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics
deseq2
PHYLOSEQ
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
dc
• 0
1
vote
1
reply
1.1k
views
WGCNA threshold without prior knowledge of scale-free propery
wgcna
weighted correlation network analysis
correlation matrix
scale-free topology
metagenomics
updated 5.3 years ago by
Peter Langfelder
★ 2.9k • written 5.3 years ago by
eneas_aguirre
• 0
0
votes
0
replies
1.2k
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna
transcriptome
big data
metagenomics
gene expression
6.1 years ago
jol.espinoz
▴ 40
0
votes
0
replies
1.2k
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
6.1 years ago
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 6.4 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.4 years ago by
lilianeconteville
▴ 10
4
votes
11
replies
2.1k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
ghanbari.msc
▴ 10
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.6 years ago
lauren.czaplicki
• 0
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
6.9 years ago
David
▴ 860
3
votes
5
replies
2.4k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 7.3 years ago by
Michael Love
41k • written 7.3 years ago by
Earendil
• 0
2
votes
3
replies
6.1k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 7.3 years ago by
Michael Love
41k • written 7.3 years ago by
pro_zac
• 0
0
votes
5
replies
1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
7.9 years ago
David
▴ 860
0
votes
2
replies
1.9k
views
Advice on normalization with metagenomics data
metagenome
normalization
metagenomics
7.9 years ago
David
▴ 860
4
votes
4
replies
3.3k
views
edgeR and gene filtering
edger
metagenomics
gene abundance
gene filtering
8.5 years ago
jtremblay514
• 0
0
votes
1
reply
1.3k
views
Influence of average genome size on DESeq2 results
deseq2
normalization
metagenomics
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
jessawbryant
• 0
8
votes
0
replies
3.5k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.8 years ago
Martin Morgan
25k
2
votes
8
replies
3.2k
views
edgeR for metagenomic data
edger
metagenomics
updated 8.8 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.8 years ago by
eleonoregravier
▴ 70
1
vote
5
replies
2.9k
views
baySeq issues and questions
bayseq
metagenomics
9.4 years ago • updated 9.2 years ago
lordbleys
• 0
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.4 years ago by
francesca.defilippis
▴ 100
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
9.5 years ago
patrick.schordert
▴ 30
0
votes
1
reply
1.5k
views
mouseData in heatmap of metagenomeSeq package
Metagenomics
metagenomeSeq
Metagenomics
metagenomeSeq
updated 10.1 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 10.1 years ago by
Guest User
★ 13k
35 results • Page
1 of 1
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Replies
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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