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Showing :
microbiome
•
reset
0
votes
2
replies
474
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome
DESeq2
5 months ago
anton.kratz
▴ 60
2
votes
1
reply
982
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
HULFRED
▴ 10
0
votes
0
replies
355
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
8 months ago
Mohamed
▴ 30
0
votes
1
reply
678
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 11 days ago by
President Gamer
• 0 • written 10 months ago by
abhisek001
• 0
0
votes
2
replies
1.3k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets
Microbiome
14 months ago
Elif
• 0
1
vote
0
replies
496
views
News:
Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData
Microbiome
16 months ago
Levi Waldron
★ 1.1k
0
votes
1
reply
662
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment
phylogenetic
microbiome
SummarizedExperiment
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
Muhammad
• 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 20 months ago by
Marcel Ramos
690 • written 20 months ago by
kikiki
• 0
2
votes
1
reply
1.6k
views
Deseq2 for 16s Data
Microbiome
16s
Deseq2
16srRNA
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
Katelyn
▴ 10
0
votes
1
reply
776
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
570
views
pairwise within sample
DESeq2
microbiome
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
laubitz
• 0
0
votes
1
reply
884
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
1
reply
856
views
Adding insect abundance data to SparCC Analysis
sparcc
Microbiome
microbiomeExplorer
MicrobiomeData
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
GlycineMax
• 0
0
votes
0
replies
949
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
0
replies
992
views
News:
Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome
news
Conference
3.2 years ago
Matthew Ritchie
▴ 1000
0
votes
2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome
edgeR
3.2 years ago
Pozdrawiam
• 0
1
vote
3
replies
6.8k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
updated 19 months ago by
adR
▴ 30 • written 3.5 years ago by
Daniel
• 0
0
votes
2
replies
1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2
microbiome
R
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
greenm11
• 0
0
votes
2
replies
829
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
931
views
Job:
Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq
DNA-seq
ATAC-seq
proteomics
microbiome
Job
4.3 years ago
lhuang7
▴ 50
1
vote
0
replies
866
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
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2
microbiome
sequencing
4.8 years ago
zhigang.li
• 0
0
votes
2
replies
1.5k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2
microbiome
updated 4.9 years ago by
swbarnes2
★ 1.3k • written 4.9 years ago by
ehickman
• 0
0
votes
0
replies
890
views
Aldex2 feature request - controlling for additional variables
ALDEx2
ALDEx
microbiome
16s
5.4 years ago
mstagliamonte
▴ 10
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
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
41k • written 5.5 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
1.3k
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
6.2 years ago
Jenny Drnevich
★ 2.0k
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2
R
microbiome
phyloseq
qiime
updated 6.4 years ago by
Michael Love
41k • written 6.4 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
3.3k
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
6.9 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
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
7.0 years ago
stats134711
• 0
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
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
7.4 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 7.6 years ago by
Steve Lianoglou
★ 13k • written 7.6 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
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
7.7 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 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
pjgalli2
• 0
0
votes
5
replies
1.5k
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
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
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq
microbiome
updated 16 months ago by
Muhammad
• 0 • written 9.2 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq
microbiome
updated 9.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.3 years ago by
noelle.noyes
▴ 30
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
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
9.3 years ago
noelle.noyes
▴ 30
2
votes
2
replies
1.5k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq
microbiome
9.3 years ago
noelle.noyes
▴ 30
50 results • Page
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Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
What I meant is even after deleting the NCBI.sqlite file, and re-running the script, an empty NCBI.sqlite file (0 kb) is created which is c…
Votes
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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