Showing : microbiome • reset
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680
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 12 days ago by • 0 • written 10 months ago by • 0
0
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2
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475
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DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
5 months ago anton.kratz ▴ 60
2
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1
reply
985
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.0k • written 7 months ago by ▴ 10
0
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0
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356
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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
8 months ago Mohamed ▴ 30
0
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2
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1.3k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
14 months ago Elif • 0
1
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0
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497
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
16 months ago Levi Waldron ★ 1.1k
1
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3
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6.8k
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 19 months ago by ▴ 30 • written 3.5 years ago by • 0
0
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1
reply
667
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 19 months ago by 65k • written 19 months ago by • 0
0
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3
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1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 20 months ago by 690 • written 20 months ago by • 0
2
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1
reply
1.6k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.0 years ago by 41k • written 2.0 years ago by ▴ 10
0
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1
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779
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
0
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1
reply
572
views
pairwise within sample
DESeq2 microbiome
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
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1
reply
885
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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1
reply
857
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
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0
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951
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
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0
replies
992
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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
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2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.2 years ago Pozdrawiam • 0
0
votes
2
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1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
0
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1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.1 years ago by • 0 • written 7.4 years ago by • 0
0
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2
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830
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 4.2 years ago by 41k • written 4.2 years ago by ▴ 10
0
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0
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933
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
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2
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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 ★ 1.3k • written 4.9 years ago by • 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
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1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.4 years ago slizo001 • 0
2
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1
reply
1.1k
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Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 850
0
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1
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1.0k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
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1
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1.6k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
0
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0
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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
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0
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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
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1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
1
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1
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1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.4 years ago by ▴ 280 • written 6.4 years ago by ▴ 10
3
votes
2
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3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.6 years ago by 41k • written 6.6 years ago by • 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
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3
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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 ★ 13k • written 7.0 years ago by • 0
1
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1
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3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 0
0
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2
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1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.4 years ago Brian Smith ▴ 120
6
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1
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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 ★ 13k • written 7.6 years ago by ▴ 20
0
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5
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3.5k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.6 years ago by ▴ 280 • written 7.7 years ago by • 0
0
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8
replies
3.2k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.7 years ago by ★ 13k • written 10.4 years ago by 41k
0
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0
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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 41k • written 7.8 years ago by • 0
0
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5
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1.5k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 10
2
votes
1
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1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.6 years ago by 41k • written 8.6 years ago by • 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 • 0 • written 9.2 years ago by ▴ 30
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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