Showing : Microbiome • reset
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967
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 12 months ago by 68k • written 12 months ago by • 0
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3
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1.7k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 15 months ago by • 0 • written 2.4 years ago by • 0
1
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1
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598
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 18 months ago by ▴ 40 • written 18 months ago by ★ 1.6k
0
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2
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1.3k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
23 months ago anton.kratz ▴ 60
2
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1
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2.3k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by ▴ 10
0
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0
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824
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.2 years ago Mohamed ▴ 30
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2
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2.9k
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
2.7 years ago Elif • 0
1
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0
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914
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
2.9 years ago Levi Waldron ★ 1.1k
1
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3
replies
9.1k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 3.1 years ago by ▴ 40 • written 5.0 years ago by • 0
0
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1
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1.2k
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
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3
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2.6k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 3.2 years ago by 700 • written 3.2 years ago by • 0
2
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1
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2.8k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
0
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1
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1.3k
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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1
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907
views
pairwise within sample
DESeq2 microbiome
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
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1
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1.4k
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
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1
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1.3k
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
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0
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1.5k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
4.3 years ago GlycineMax • 0
0
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0
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1.4k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
4.7 years ago Matthew Ritchie ▴ 1000
0
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2
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1.6k
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Question: export edgeR normalised OTU table
microbiome edgeR
4.7 years ago Pozdrawiam • 0
0
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2
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2.4k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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1
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1.6k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.6 years ago by • 0 • written 8.9 years ago by • 0
0
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2
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1.3k
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 10
0
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0
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1.3k
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.8 years ago lhuang7 ▴ 50
1
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0
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1.3k
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
6.0 years ago supindab ▴ 10
0
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2
replies
1.8k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
6.3 years ago zhigang.li • 0
0
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2
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2.0k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
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0
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1.3k
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Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
6.9 years ago mstagliamonte ▴ 10
0
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1
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1.6k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.9 years ago slizo001 • 0
2
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1
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1.5k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 7.0 years ago by ★ 3.6k • written 7.0 years ago by ▴ 870
0
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1
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1.4k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
0
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1
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2.0k
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DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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0
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1.8k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
7.6 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.7k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
7.7 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.8k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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1
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2.3k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by ▴ 10
3
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2
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4.2k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
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6
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2.1k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
8.4 years ago lanhuong ▴ 20
0
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3
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2.2k
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Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 8.5 years ago by ★ 13k • written 8.5 years ago by • 0
1
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1
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4.3k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.5 years ago stats134711 • 0
0
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2
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1.9k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.9 years ago Brian Smith ▴ 120
8
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1
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4.3k
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 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 30
0
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5
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4.2k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by • 0
0
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8
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4.0k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 9.2 years ago by ★ 13k • written 11.9 years ago by 43k
0
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0
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1.6k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
9.2 years ago Daniel Brewer ▴ 100
4
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3
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2.6k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 9.3 years ago by 43k • written 9.3 years ago by • 0
0
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5
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2.0k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 10
2
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1
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2.2k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 10.1 years ago by 43k • written 10.1 years ago by • 0
1
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2
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2.3k
views
Normalization factors in metagenomeSeq
microbiome
10.5 years ago jovel_juan ▴ 30
2
votes
4
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2.9k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.9 years ago by • 0 • written 10.7 years ago by ▴ 30
1
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1
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3.7k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.8 years ago by ▴ 280 • written 10.8 years ago by ▴ 30
61 results • Page 1 of 2
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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