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Metagenomics
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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
357
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
0
votes
1
reply
682
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 12 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
1
vote
4
replies
745
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
14 months ago • updated 13 months ago
Michael
• 0
0
votes
0
replies
537
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
1
vote
0
replies
611
views
Shotgun metagenomics data analysis
Metagenomics
abundance
18 months ago
YASIR
▴ 10
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
0
votes
1
reply
897
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
21 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
818
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
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
952
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
1
reply
767
views
FDR Correction
dada2
Metagenomics
DESeq2
updated 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
GlycineMax
• 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
0
replies
986
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
15
votes
4
replies
32k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 3.7 years ago by
Ram
▴ 190 • written 3.7 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
1.2k
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
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
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
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
2.2k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
ghanbari.msc
▴ 10
1
vote
3
replies
1.9k
views
Error bars on DESeq2 visuals
deseq2
metagenomics
phyloseq
ggplot2
6.7 years ago
lauren.czaplicki
• 0
0
votes
0
replies
1.3k
views
Phylogenetic tree from marker genes
ape
phyloseq
dist
metagenomics
7.0 years ago
David
▴ 860
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
2
votes
3
replies
6.2k
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
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
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
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
3.6k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.8 years ago
Martin Morgan
25k
2
votes
8
replies
3.3k
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
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
5
replies
2.9k
views
baySeq issues and questions
bayseq
metagenomics
9.5 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
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
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Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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