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Microbiome
•
reset
0
votes
2
replies
427
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome
DESeq2
4 months ago
anton.kratz
▴ 60
2
votes
1
reply
893
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
328
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
1
reply
556
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
written 9 months ago by
abhisek001
• 0
0
votes
2
replies
1.2k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets
Microbiome
13 months ago
Elif
• 0
1
vote
0
replies
470
views
News:
Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData
Microbiome
15 months ago
Levi Waldron
★ 1.1k
1
vote
3
replies
6.7k
views
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
0
votes
1
reply
626
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment
phylogenetic
microbiome
SummarizedExperiment
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Muhammad
• 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
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
0
votes
1
reply
743
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome
LRT
DESeq2
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Mir
• 0
0
votes
1
reply
549
views
pairwise within sample
DESeq2
microbiome
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
laubitz
• 0
0
votes
1
reply
857
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
0
votes
1
reply
824
views
Adding insect abundance data to SparCC Analysis
sparcc
Microbiome
microbiomeExplorer
MicrobiomeData
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
GlycineMax
• 0
0
votes
0
replies
914
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
0
replies
967
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
2
replies
1.1k
views
Question: export edgeR normalised OTU table
microbiome
edgeR
3.2 years ago
Pozdrawiam
• 0
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
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
812
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2
16s
microbiome
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
mstagliamonte
▴ 10
0
votes
0
replies
908
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
1
vote
0
replies
835
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
0
votes
2
replies
1.2k
views
DESeq2 error on analyzing microbiome data
deseq2
microbiome
sequencing
4.7 years ago
zhigang.li
• 0
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
0
replies
873
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
5.3 years ago
mstagliamonte
▴ 10
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
994
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
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
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
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
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
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
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
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
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
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
7.3 years ago
Brian Smith
▴ 120
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
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
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
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
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
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
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
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.0 years ago
jovel_juan
▴ 30
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
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
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
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
9.2 years ago
noelle.noyes
▴ 30
50 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Answer: Merging featureCounts output for different species
by
Michael Love
41k
Bioconductor support site is for posting questions about software. Try biostars.
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
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