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Metagenomics
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Job:
Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics
curatedMetagenomicData
bugsigdbr
written 12 weeks ago by
Levi Waldron
★ 1.1k
0
votes
0
replies
321
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
2
replies
519
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
1
vote
4
replies
692
views
How do I design my DESEQ experiment?
DESeq2
Metagenomics
12 months ago
Michael
• 0
0
votes
0
replies
488
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
569
views
Shotgun metagenomics data analysis
Metagenomics
abundance
16 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
★ 3.9k • written 19 months ago by
Muhammad
• 0
0
votes
1
reply
865
views
Job:
'Omics data analyst for HPCBio, University of Illinois
Metagenomics
GenomicVariation
Genomics
RNASeq
ChIPSeq
20 months ago • updated 19 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
754
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Aditya
• 0
0
votes
1
reply
2.1k
views
Import MetaPhlAn3 to Phyloseq
Metaphlan3
Metagenomics
phyloseq
updated 2.7 years ago by
Levi Waldron
★ 1.1k • written 2.7 years ago by
Saraswati
• 0
0
votes
0
replies
908
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.7 years ago
GlycineMax
• 0
0
votes
1
reply
724
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 2.9 years ago by
Michael Love
41k • written 2.9 years ago by
Tom
• 0
0
votes
0
replies
943
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 3.6 years ago by
Michael Love
41k • written 3.6 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 6.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.3 years ago by
lilianeconteville
▴ 10
4
votes
11
replies
2.1k
views
DESeq2 on 16S copy number corrected genes
deseq2
metagenomics
updated 6.5 years ago by
Michael Love
41k • written 6.6 years ago by
ghanbari.msc
▴ 10
1
vote
3
replies
1.8k
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
8.4 years ago
jtremblay514
• 0
0
votes
1
reply
1.3k
views
Influence of average genome size on DESeq2 results
deseq2
normalization
metagenomics
updated 8.4 years ago by
Michael Love
41k • written 8.4 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
8.7 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
2.8k
views
baySeq issues and questions
bayseq
metagenomics
9.4 years ago • updated 9.1 years ago
lordbleys
• 0
0
votes
2
replies
4.4k
views
Pathway enrichment in bacteria metagenomes
pathways
metagenomics
updated 9.3 years ago by
Luo Weijun
★ 1.6k • written 9.3 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 10.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 10.0 years ago by
Guest User
★ 13k
35 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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