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microbiome
•
reset
0
votes
2
replies
416
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome
DESeq2
4 months ago
anton.kratz
▴ 60
2
votes
1
reply
857
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 6 months ago by
ATpoint
★ 3.9k • written 6 months ago by
HULFRED
▴ 10
0
votes
0
replies
321
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
2
replies
519
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
464
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
6.6k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome
DESeq2
updated 17 months ago by
adR
▴ 30 • written 3.4 years ago by
Daniel
• 0
0
votes
1
reply
618
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
1.5k
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 19 months ago by
Marcel Ramos
680 • 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
733
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
544
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
851
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
820
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
908
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.7 years ago
GlycineMax
• 0
0
votes
0
replies
963
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
3.1 years ago
Pozdrawiam
• 0
0
votes
2
replies
1.5k
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
807
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2
16s
microbiome
updated 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
mstagliamonte
▴ 10
0
votes
0
replies
904
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
830
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
4.4 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
870
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
★ 3.5k • written 5.4 years ago by
W. Evan Johnson
▴ 850
0
votes
1
reply
990
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 5.8 years ago by
Michael Love
41k • written 5.8 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 6.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.3 years ago by
lilianeconteville
▴ 10
3
votes
2
replies
3.2k
views
DESeq2 iterative size factor normalization did not converge
deseq2
microbiome
phyloseq
updated 6.5 years ago by
Michael Love
41k • written 6.5 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 6.9 years ago by
Wolfgang Huber
★ 13k • written 6.9 years ago by
stats134711
• 0
1
vote
1
reply
3.4k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome
normalization
variancestabilizingtransformation
phyloseq
6.9 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
3.1k
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 7.5 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 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
drei
• 0
1
vote
2
replies
1.8k
views
Normalization factors in metagenomeSeq
microbiome
8.9 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: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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