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Showing :
Microbiome
•
reset
0
votes
2
replies
76
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
3 days ago • updated 2 days ago
kikiki
• 0
1
vote
1
reply
235
views
Deseq2 for 16s Data
Microbiome
16s
Deseq2
16srRNA
updated 3 months ago by
Michael Love
37k • written 3 months ago by
Katelyn
• 0
0
votes
1
reply
246
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome
LRT
DESeq2
updated 6 months ago by
Michael Love
37k • written 6 months ago by
Mir
• 0
0
votes
1
reply
194
views
pairwise within sample
DESeq2
microbiome
updated 11 months ago by
Michael Love
37k • written 11 months ago by
laubitz
• 0
0
votes
1
reply
273
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData
microbiome
offtopic
updated 12 months ago by
James W. MacDonald
60k • written 12 months ago by
gwagz8
• 0
0
votes
1
reply
333
views
Adding insect abundance data to SparCC Analysis
sparcc
Microbiome
microbiomeExplorer
MicrobiomeData
updated 13 months ago by
Kevin Blighe
3.6k • written 13 months ago by
GlycineMax
• 0
0
votes
0
replies
311
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
13 months ago
GlycineMax
• 0
0
votes
0
replies
453
views
News:
Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome
news
Conference
18 months ago
Matthew Ritchie
▴ 1000
0
votes
2
replies
522
views
Question: export edgeR normalised OTU table
microbiome
edgeR
18 months ago
Pozdrawiam
• 0
1
vote
2
replies
2.4k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
21 months ago
Daniel
• 0
0
votes
2
replies
731
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2
microbiome
R
updated 23 months ago by
Michael Love
37k • written 23 months ago by
greenm11
• 0
0
votes
1
reply
779
views
MetagenomeSeq: analysing paired samples
metagenomeseq
paired samples
microbiome
updated 2.3 years ago by
jananee15
• 0 • written 5.7 years ago by
marypadilha
• 0
0
votes
2
replies
312
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2
16s
microbiome
updated 2.5 years ago by
Michael Love
37k • written 2.5 years ago by
mstagliamonte
• 0
0
votes
0
replies
464
views
Job:
Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq
DNA-seq
ATAC-seq
proteomics
microbiome
Job
2.6 years ago
lhuang7
▴ 50
1
vote
0
replies
413
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
2.8 years ago
supindab
▴ 10
0
votes
2
replies
573
views
DESeq2 error on analyzing microbiome data
deseq2
microbiome
sequencing
3.1 years ago
zhigang.li
• 0
0
votes
2
replies
630
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2
microbiome
updated 3.1 years ago by
swbarnes2
★ 1.1k • written 3.1 years ago by
ehickman
• 0
0
votes
0
replies
458
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
3.6 years ago
mstagliamonte
• 0
0
votes
1
reply
567
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error
metagenomeseq
microbiome
3.7 years ago
slizo001
• 0
2
votes
1
reply
599
views
Rsubread for microbiome data analysis: genome >4GB
alignment
rsubread
microbiome
updated 3.8 years ago by
Wei Shi
★ 3.5k • written 3.8 years ago by
W. Evan Johnson
▴ 840
0
votes
1
reply
509
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 3.8 years ago by
Michael Love
37k • written 3.8 years ago by
FaisalH
• 0
0
votes
1
reply
964
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2
microbiome
fungi
fungal microbiome
updated 4.2 years ago by
Michael Love
37k • written 4.2 years ago by
david.gramaje
• 0
0
votes
0
replies
708
views
Job:
EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome
epigenomics
bioinformatics
analyst
NGS
Job
4.4 years ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
722
views
Job:
Bioinformatics Specialist at the University of Illinois
job
bioinformatics
microbiome
metagenomics
epigenomics
Job
4.5 years ago
Jenny Drnevich
★ 2.0k
1
vote
1
reply
852
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 4.7 years ago by
Michael Love
37k • written 4.7 years ago by
ssingh59
• 0
1
vote
1
reply
1.0k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 4.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 4.7 years ago by
lilianeconteville
▴ 10
2
votes
2
replies
2.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 4.9 years ago by
Michael Love
37k • written 4.9 years ago by
couchc
• 0
0
votes
6
replies
1.0k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome
16s
deseq2
differential gene expression
5.2 years ago
lanhuong
▴ 20
0
votes
3
replies
1.0k
views
Where to find open access microbiome data for case-control comparative study?
microbiome
data analysis
data request
updated 5.3 years ago by
Wolfgang Huber
13k • written 5.3 years ago by
stats134711
• 0
1
vote
1
reply
2.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
5.3 years ago
stats134711
• 0
0
votes
2
replies
1.0k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
5.7 years ago
Brian Smith
▴ 120
3
votes
1
reply
1.9k
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 5.8 years ago by
Steve Lianoglou
13k • written 5.8 years ago by
tealfurn
• 0
0
votes
5
replies
2.6k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 5.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 5.9 years ago by
jbatsx
• 0
0
votes
8
replies
2.5k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome
DESeq2
Microbiome
DESeq2
updated 6.0 years ago by
Wolfgang Huber
13k • written 8.7 years ago by
Michael Love
37k
0
votes
0
replies
879
views
Job:
2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer
microbiome
postdoc
UK
prostate cancer
Job
6.0 years ago
Daniel Brewer
▴ 90
4
votes
3
replies
1.4k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2
microbiome
zero-inflated
updated 6.1 years ago by
Michael Love
37k • written 6.1 years ago by
pjgalli2
• 0
0
votes
5
replies
1.0k
views
deseq2 analysis, accounting for pen effect
deseq2
microbiome
updated 6.8 years ago by
Steve Lianoglou
13k • written 6.8 years ago by
bjarke
▴ 10
2
votes
1
reply
1.4k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2
differential expression
microbiome
updated 6.9 years ago by
Michael Love
37k • written 6.9 years ago by
drei
• 0
1
vote
2
replies
1.4k
views
Normalization factors in metagenomeSeq
microbiome
7.3 years ago
jovel_juan
▴ 10
2
votes
3
replies
1.6k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq
microbiome
updated 7.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.5 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
2.3k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq
microbiome
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
1.1k
views
Problem reproducing metagenomeSeq tutorial example
metagenome
microbiome
metagenomeseq
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
jovel_juan
▴ 10
2
votes
2
replies
842
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
7.6 years ago
noelle.noyes
▴ 30
2
votes
2
replies
1.1k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq
microbiome
7.6 years ago
noelle.noyes
▴ 30
1
vote
1
reply
1.3k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq
microbiome
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
noelle.noyes
▴ 30
0
votes
1
reply
915
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 7.8 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.8 years ago by
songeric1107
• 0
1
vote
2
replies
4.1k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2
normalization
microbiome
updated 7.9 years ago by
Michael Love
37k • written 7.9 years ago by
btemperton
• 0
0
votes
3
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome
Normalization
Clustering
DESeq
DESeq2
Microbiome
Normalization
Clustering
DESeq
updated 8.3 years ago by
Sophie Josephine Weiss
▴ 130 • written 8.3 years ago by
Michael Love
37k
2
votes
19
replies
1.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome
DESeq
Microbiome
DESeq
updated 8.3 years ago by
Michael Love
37k • written 8.3 years ago by
Sophie Josephine Weiss
▴ 130
0
votes
0
replies
2.2k
views
Pathview with non-KEGG organisms?
Microbiome
Pathways
GO
Visualization
Organism
graph
gage
pathview
Microbiome
Pathways
GO
9.0 years ago
Luo Weijun
★ 1.5k
50 results • Page
1 of 1
Recent ...
Replies
Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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▴ 1000
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▴ 10
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