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microbiome
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3
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7.0k
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DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
updated 19 months ago by
adR
▴ 30 • written 3.6 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 9.6 years ago by
Michael Love
42k • written 9.6 years ago by
btemperton
• 0
0
votes
5
replies
3.6k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 7.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.7 years ago by
jbatsx
• 0
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.1 years ago
stats134711
• 0
0
votes
3
replies
3.4k
views
phyloseq/DESeq gives negative transformed values
Microbiome
Normalization
Clustering
DESeq
DESeq2
Microbiome
Normalization
Clustering
DESeq
updated 10.0 years ago by
Sophie Josephine Weiss
▴ 130 • written 10.0 years ago by
Michael Love
42k
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.7 years ago by
Michael Love
42k • written 6.7 years ago by
couchc
• 0
0
votes
8
replies
3.3k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome
DESeq2
Microbiome
DESeq2
updated 7.8 years ago by
Wolfgang Huber
★ 13k • written 10.5 years ago by
Michael Love
42k
6
votes
1
reply
3.3k
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 7.6 years ago by
Steve Lianoglou
★ 13k • written 7.6 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
11.6 years ago
Dan Tenenbaum
★ 8.2k
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq
microbiome
updated 9.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.3 years ago by
noelle.noyes
▴ 30
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome
DESeq
Microbiome
DESeq
updated 10.1 years ago by
Michael Love
42k • written 10.1 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
10.8 years ago
Luo Weijun
★ 1.6k
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq
microbiome
updated 17 months ago by
Muhammad
• 0 • written 9.3 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 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
pjgalli2
• 0
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.1 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 8.7 years ago by
Michael Love
42k • written 8.7 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 6.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.5 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 9.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.3 years ago by
noelle.noyes
▴ 30
2
votes
1
reply
1.7k
views
Deseq2 for 16s Data
Microbiome
16s
Deseq2
16srRNA
updated 2.1 years ago by
Michael Love
42k • written 2.1 years ago by
Katelyn
▴ 10
0
votes
3
replies
1.7k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 21 months ago by
Marcel Ramos
690 • written 21 months ago by
kikiki
• 0
0
votes
1
reply
1.6k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2
microbiome
fungi
fungal microbiome
updated 6.0 years ago by
Michael Love
42k • written 6.0 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 7.1 years ago by
Wolfgang Huber
★ 13k • written 7.1 years ago by
stats134711
• 0
0
votes
2
replies
1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2
microbiome
R
updated 3.7 years ago by
Michael Love
42k • written 3.7 years ago by
greenm11
• 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
6.9 years ago
lanhuong
▴ 20
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome
microbiome
metagenomeseq
updated 9.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.3 years ago by
jovel_juan
▴ 30
2
votes
2
replies
1.6k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq
microbiome
9.3 years ago
noelle.noyes
▴ 30
0
votes
5
replies
1.6k
views
deseq2 analysis, accounting for pen effect
deseq2
microbiome
updated 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
bjarke
▴ 10
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
7.5 years ago
Brian Smith
▴ 120
0
votes
2
replies
1.5k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2
microbiome
updated 4.9 years ago by
swbarnes2
★ 1.4k • written 4.9 years ago by
ehickman
• 0
0
votes
3
replies
1.4k
views
Correlation analysis
Microbiome
HIV
Microbiome
HIV
updated 12.5 years ago by
Sean Davis
21k • written 12.5 years ago by
Minh Bui
▴ 20
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
ssingh59
• 0
0
votes
2
replies
1.4k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets
Microbiome
15 months ago
Elif
• 0
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
9.3 years ago
noelle.noyes
▴ 30
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
7.8 years ago
Daniel Brewer
▴ 100
0
votes
2
replies
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2
microbiome
sequencing
4.9 years ago • updated 4.8 years ago
zhigang.li
• 0
0
votes
0
replies
1.3k
views
Job:
EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome
epigenomics
bioinformatics
analyst
NGS
Job
6.1 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
1.3k
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
6.3 years ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq
paired samples
microbiome
updated 4.1 years ago by
jananee15
• 0 • written 7.4 years ago by
marypadilha
• 0
0
votes
1
reply
1.2k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 9.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.5 years ago by
songeric1107
• 0
0
votes
2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome
edgeR
3.3 years ago
Pozdrawiam
• 0
0
votes
1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error
metagenomeseq
microbiome
5.4 years ago
slizo001
• 0
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment
rsubread
microbiome
updated 5.5 years ago by
Wei Shi
★ 3.6k • written 5.5 years ago by
W. Evan Johnson
▴ 850
2
votes
1
reply
1.1k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
HULFRED
▴ 10
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
FaisalH
• 0
0
votes
0
replies
1.0k
views
News:
Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome
news
Conference
3.3 years ago
Matthew Ritchie
▴ 1000
0
votes
0
replies
976
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.9 years ago
GlycineMax
• 0
0
votes
0
replies
948
views
Job:
Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq
DNA-seq
ATAC-seq
proteomics
microbiome
Job
4.4 years ago
lhuang7
▴ 50
0
votes
1
reply
918
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData
microbiome
offtopic
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
gwagz8
• 0
0
votes
0
replies
914
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
5.4 years ago
mstagliamonte
▴ 10
0
votes
1
reply
888
views
Adding insect abundance data to SparCC Analysis
sparcc
Microbiome
microbiomeExplorer
MicrobiomeData
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
GlycineMax
• 0
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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