Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
metagenomics
•
reset
1
vote
5
replies
2.9k
views
baySeq issues and questions
bayseq
metagenomics
9.4 years ago • updated 9.2 years ago
lordbleys
• 0
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
9.6 years ago
patrick.schordert
▴ 30
2
votes
8
replies
3.3k
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
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
8.0 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
2
votes
3
replies
6.1k
views
DESEq2 error when performing exploratory analysis with no replicates
software error
deseq2
metagenomics
updated 7.4 years ago by
Michael Love
41k • written 7.4 years ago by
pro_zac
• 0
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.7 years ago
lauren.czaplicki
• 0
4
votes
11
replies
2.2k
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
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
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
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 5.3 years ago by
Peter Langfelder
★ 3.0k • written 5.3 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 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
dc
• 0
15
votes
4
replies
32k
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
667
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 6 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
0
votes
1
reply
801
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
Aditya
• 0
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
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
3
votes
3
replies
1.2k
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
1
reply
756
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
GlycineMax
• 0
1
vote
4
replies
733
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
13 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 20 months ago by
ATpoint
★ 4.0k • written 20 months ago by
Muhammad
• 0
3
votes
5
replies
2.4k
views
DESeq2 to clustered metagenomic data
deseq2
metagenomics
updated 7.4 years ago by
Michael Love
41k • written 7.4 years ago by
Earendil
• 0
0
votes
0
replies
351
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
8 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
8.8 years ago
Martin Morgan
25k
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
7.0 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
6.2 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
6.2 years ago
jol.espinoz
▴ 40
0
votes
0
replies
975
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.1 years ago
jol.espinoz
▴ 40
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
1
vote
0
replies
601
views
Shotgun metagenomics data analysis
Metagenomics
abundance
17 months ago
YASIR
▴ 10
0
votes
1
reply
889
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
21 months ago • updated 20 months ago
Jenny Drnevich
★ 2.0k
0
votes
2
replies
494
views
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
940
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
0
replies
529
views
ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics
IQLR
ALDEx2
16 months ago
cwarden45
• 0
35 results • Page
1 of 1
Recent ...
Replies
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR
by
Gordon Smyth
50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Answer: Log-cpm values from limma
by
Gordon Smyth
50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Awards
• All
Popular Question
to
Gordon Smyth
50k
Scholar
to
Peter Hickey
▴ 740
Popular Question
to
sropri
• 0
Popular Question
to
W. Evan Johnson
▴ 850
Popular Question
to
Alejandro Reyes
★ 1.9k
Locations
• All
France,
2 minutes ago
France,
9 minutes ago
WEHI, Melbourne, Australia,
13 minutes ago
France/Marseille/Inserm,
18 minutes ago
Spain,
33 minutes ago
Traffic: 820 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6