Showing : microbiome • reset
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490
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 5 months ago by 68k • written 5 months ago by • 0
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3
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1.4k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 7 months ago by • 0 • written 21 months ago by • 0
1
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1
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418
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 10 months ago by ▴ 40 • written 10 months ago by ★ 1.6k
0
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2
replies
885
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DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
15 months ago anton.kratz ▴ 60
2
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1
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1.9k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 17 months ago by ★ 4.7k • written 17 months ago by ▴ 10
0
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0
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673
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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
18 months ago Mohamed ▴ 30
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2
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2.3k
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
2.1 years ago Elif • 0
1
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0
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720
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
2.2 years ago Levi Waldron ★ 1.1k
1
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3
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8.5k
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 2.4 years ago by ▴ 40 • written 4.4 years ago by • 0
0
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1
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1.0k
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
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3
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2.3k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 2.6 years ago by 700 • written 2.6 years ago by • 0
2
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1
reply
2.4k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 10
0
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1
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1.1k
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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1
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779
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pairwise within sample
DESeq2 microbiome
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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1
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1.2k
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
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1.1k
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
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0
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1.3k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.7 years ago GlycineMax • 0
0
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0
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1.3k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
4.1 years ago Matthew Ritchie ▴ 1000
0
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2
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1.4k
views
Question: export edgeR normalised OTU table
microbiome edgeR
4.1 years ago Pozdrawiam • 0
0
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2
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2.1k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
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1
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1.5k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.9 years ago by • 0 • written 8.2 years ago by • 0
0
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2
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1.1k
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 10
0
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0
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1.2k
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.2 years ago lhuang7 ▴ 50
1
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0
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1.1k
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
5.4 years ago supindab ▴ 10
0
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2
replies
1.6k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
5.6 years ago zhigang.li • 0
0
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2
replies
1.8k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by • 0
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0
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1.1k
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
6.2 years ago mstagliamonte ▴ 10
0
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1
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1.4k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.2 years ago slizo001 • 0
2
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1
reply
1.4k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 6.3 years ago by ★ 3.6k • written 6.3 years ago by ▴ 870
0
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1
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1.2k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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1
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1.9k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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0
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1.6k
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Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
6.9 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.5k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
7.1 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.6k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
1
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1
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2.1k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 10
3
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2
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4.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
0
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6
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1.9k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
7.7 years ago lanhuong ▴ 20
0
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3
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1.9k
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Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
1
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1
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4.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.9 years ago stats134711 • 0
0
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2
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1.8k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.3 years ago Brian Smith ▴ 120
8
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1
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4.0k
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 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 30
0
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5
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3.9k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by • 0
0
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8
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3.7k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 8.5 years ago by ★ 13k • written 11.3 years ago by 43k
0
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0
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1.5k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
8.6 years ago Daniel Brewer ▴ 100
4
votes
3
replies
2.3k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
0
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5
replies
1.8k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 9.3 years ago by ★ 13k • written 9.3 years ago by ▴ 10
2
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1
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2.0k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
1
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2
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2.2k
views
Normalization factors in metagenomeSeq
microbiome
9.9 years ago jovel_juan ▴ 30
2
votes
4
replies
2.7k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.2 years ago by • 0 • written 10.1 years ago by ▴ 30
1
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1
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3.4k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
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Popular Question to Stefano Mangiola ▴ 40
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