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microbiome
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6.7k
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DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
updated 18 months ago by
adR
▴ 30 • written 3.4 years ago by
Daniel
• 0
1
vote
2
replies
4.6k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2
normalization
microbiome
updated 9.5 years ago by
Michael Love
41k • written 9.5 years ago by
btemperton
• 0
0
votes
5
replies
3.5k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
jbatsx
• 0
1
vote
1
reply
3.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.0 years ago
stats134711
• 0
0
votes
3
replies
3.3k
views
phyloseq/DESeq gives negative transformed values
Microbiome
Normalization
Clustering
DESeq
DESeq2
Microbiome
Normalization
Clustering
DESeq
updated 9.9 years ago by
Sophie Josephine Weiss
▴ 130 • written 9.9 years ago by
Michael Love
41k
3
votes
2
replies
3.2k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
couchc
• 0
0
votes
8
replies
3.2k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome
DESeq2
Microbiome
DESeq2
updated 7.6 years ago by
Wolfgang Huber
★ 13k • written 10.3 years ago by
Michael Love
41k
6
votes
1
reply
3.2k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma
rna-seq
multi-mapped reads
normalization
microbiome
updated 7.5 years ago by
Steve Lianoglou
★ 13k • written 7.5 years ago by
tealfurn
▴ 20
0
votes
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews
SNP
Transcription
Sequencing
miRNA
Microbiome
Microarray
qPCR
Genetics
Coverage
11.5 years ago
Dan Tenenbaum
★ 8.2k
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq
microbiome
updated 9.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.2 years ago by
noelle.noyes
▴ 30
2
votes
19
replies
2.8k
views
phyloseq/DESeq gives negative transformed values
Microbiome
DESeq
Microbiome
DESeq
updated 9.9 years ago by
Michael Love
41k • written 10.0 years ago by
Sophie Josephine Weiss
▴ 130
0
votes
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome
Pathways
GO
Visualization
Organism
graph
gage
pathview
Microbiome
Pathways
GO
10.7 years ago
Luo Weijun
★ 1.6k
2
votes
4
replies
2.2k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq
microbiome
updated 15 months ago by
Muhammad
• 0 • written 9.1 years ago by
noelle.noyes
▴ 30
4
votes
3
replies
2.0k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2
microbiome
zero-inflated
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
pjgalli2
• 0
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.0 years ago
jovel_juan
▴ 30
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2
differential expression
microbiome
updated 8.6 years ago by
Michael Love
41k • written 8.6 years ago by
drei
• 0
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
1
vote
1
reply
1.7k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq
microbiome
updated 9.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.2 years ago by
noelle.noyes
▴ 30
0
votes
1
reply
1.6k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2
microbiome
fungi
fungal microbiome
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
david.gramaje
• 0
0
votes
3
replies
1.6k
views
Where to find open access microbiome data for case-control comparative study?
microbiome
data analysis
data request
updated 7.0 years ago by
Wolfgang Huber
★ 13k • written 7.0 years ago by
stats134711
• 0
0
votes
6
replies
1.6k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome
16s
deseq2
differential gene expression
6.8 years ago
lanhuong
▴ 20
0
votes
2
replies
1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2
microbiome
R
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
greenm11
• 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 19 months ago by
Marcel Ramos
690 • written 19 months ago by
kikiki
• 0
1
vote
1
reply
1.5k
views
Problem reproducing metagenomeSeq tutorial example
metagenome
microbiome
metagenomeseq
updated 9.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.2 years ago by
jovel_juan
▴ 30
2
votes
1
reply
1.5k
views
Deseq2 for 16s Data
Microbiome
16s
Deseq2
16srRNA
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Katelyn
▴ 10
2
votes
2
replies
1.5k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq
microbiome
9.2 years ago
noelle.noyes
▴ 30
0
votes
5
replies
1.5k
views
deseq2 analysis, accounting for pen effect
deseq2
microbiome
updated 8.4 years ago by
Steve Lianoglou
★ 13k • written 8.4 years ago by
bjarke
▴ 10
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
7.3 years ago
Brian Smith
▴ 120
0
votes
2
replies
1.4k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2
microbiome
updated 4.8 years ago by
swbarnes2
★ 1.3k • written 4.8 years ago by
ehickman
• 0
0
votes
3
replies
1.4k
views
Correlation analysis
Microbiome
HIV
Microbiome
HIV
updated 12.4 years ago by
Sean Davis
21k • written 12.4 years ago by
Minh Bui
▴ 20
1
vote
1
reply
1.3k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
ssingh59
• 0
0
votes
0
replies
1.3k
views
Job:
2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer
microbiome
postdoc
UK
prostate cancer
Job
7.6 years ago
Daniel Brewer
▴ 100
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
9.2 years ago
noelle.noyes
▴ 30
0
votes
2
replies
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2
microbiome
sequencing
4.7 years ago
zhigang.li
• 0
0
votes
0
replies
1.2k
views
Job:
EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome
epigenomics
bioinformatics
analyst
NGS
Job
6.0 years ago
Jenny Drnevich
★ 2.0k
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
0
votes
1
reply
1.2k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 9.4 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.4 years ago by
songeric1107
• 0
0
votes
2
replies
1.2k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets
Microbiome
13 months ago
Elif
• 0
0
votes
1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq
paired samples
microbiome
updated 4.0 years ago by
jananee15
• 0 • written 7.3 years ago by
marypadilha
• 0
0
votes
2
replies
1.1k
views
Question: export edgeR normalised OTU table
microbiome
edgeR
3.2 years ago
Pozdrawiam
• 0
0
votes
1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error
metagenomeseq
microbiome
5.3 years ago
slizo001
• 0
2
votes
1
reply
1.0k
views
Rsubread for microbiome data analysis: genome >4GB
alignment
rsubread
microbiome
updated 5.4 years ago by
Wei Shi
★ 3.6k • written 5.4 years ago by
W. Evan Johnson
▴ 850
0
votes
1
reply
997
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
FaisalH
• 0
0
votes
0
replies
969
views
News:
Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome
news
Conference
3.1 years ago
Matthew Ritchie
▴ 1000
0
votes
0
replies
917
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
0
replies
910
views
Job:
Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq
DNA-seq
ATAC-seq
proteomics
microbiome
Job
4.2 years ago
lhuang7
▴ 50
2
votes
1
reply
897
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
HULFRED
▴ 10
0
votes
0
replies
875
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
5.3 years ago
mstagliamonte
▴ 10
0
votes
1
reply
860
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData
microbiome
offtopic
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
gwagz8
• 0
1
vote
0
replies
839
views
Job:
Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job
bioinformatician
systems biology
microbiome
genomics
Job
4.5 years ago
supindab
▴ 10
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Comment: Minfi - estimatecellscount
by
clacarion
• 0
Thank you for your response, that's what i was thinking I will try with the rgset only and come back to tell you what's happening ! Best…
Answer: Minfi - estimatecellscount
by
James W. MacDonald
65k
Don't filter first. You are likely removing the CpGs that are used to estimate the cell counts.
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
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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