Showing : Microbiome • reset
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137
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 9 days ago by ★ 3.4k • written 10 days ago by • 0
0
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0
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97
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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
5 weeks ago Mohamed ▴ 20
0
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1
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240
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
written 3 months ago by • 0
0
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2
replies
634
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
7 months ago Elif • 0
1
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0
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272
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
9 months ago Levi Waldron 1.1k
1
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3
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5.5k
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 12 months ago by ▴ 30 • written 2.9 years ago by • 0
0
votes
1
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405
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 12 months ago by 63k • written 12 months ago by • 0
0
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3
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1.0k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 13 months ago by 680 • written 13 months ago by • 0
1
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1
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1.0k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 17 months ago by 40k • written 17 months ago by • 0
0
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1
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565
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 20 months ago by 40k • written 20 months ago by • 0
0
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1
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412
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pairwise within sample
DESeq2 microbiome
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
0
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1
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644
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
0
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1
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645
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 2.2 years ago by 3.8k • written 2.2 years ago by • 0
0
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0
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691
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.3 years ago GlycineMax • 0
0
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0
replies
803
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News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
2.6 years ago Matthew Ritchie ▴ 1000
0
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2
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897
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Question: export edgeR normalised OTU table
microbiome edgeR
2.7 years ago Pozdrawiam • 0
0
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2
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1.3k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.0 years ago by 40k • written 3.0 years ago by • 0
0
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1
reply
1.0k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 3.5 years ago by • 0 • written 6.8 years ago by • 0
0
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2
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615
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 3.7 years ago by 40k • written 3.7 years ago by ▴ 10
0
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0
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767
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
3.7 years ago lhuang7 ▴ 50
1
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0
replies
672
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Job: Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job bioinformatician systems biology microbiome genomics Job
4.0 years ago supindab ▴ 10
0
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2
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1.0k
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.2 years ago zhigang.li • 0
0
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2
replies
1.2k
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by • 0
0
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0
replies
728
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Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
4.8 years ago mstagliamonte ▴ 10
0
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1
reply
907
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
4.8 years ago slizo001 • 0
2
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1
reply
867
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 4.9 years ago by ★ 3.5k • written 4.9 years ago by ▴ 850
0
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1
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823
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 4.9 years ago by 40k • written 4.9 years ago by • 0
0
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1
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1.4k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 5.4 years ago by 40k • written 5.4 years ago by • 0
0
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0
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1.0k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
5.5 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.0k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
5.6 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.2k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 5.8 years ago by 40k • written 5.8 years ago by • 0
1
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1
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1.4k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 5.9 years ago by ▴ 280 • written 5.9 years ago by ▴ 10
3
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2
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2.8k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.1 years ago by 40k • written 6.1 years ago by • 0
0
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6
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1.4k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
6.3 years ago lanhuong ▴ 20
0
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3
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1.4k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 6.5 years ago by 13k • written 6.5 years ago by • 0
1
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1
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3.1k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
6.5 years ago stats134711 • 0
0
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2
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1.3k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
6.8 years ago Brian Smith ▴ 120
6
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1
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2.7k
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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 7.0 years ago by 13k • written 7.0 years ago by ▴ 20
0
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5
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3.2k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by • 0
0
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8
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2.9k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.1 years ago by 13k • written 9.8 years ago by 40k
0
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0
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1.1k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
7.1 years ago Daniel Brewer ▴ 100
4
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3
replies
1.8k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 7.2 years ago by 40k • written 7.2 years ago by • 0
0
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5
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1.3k
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deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 7.9 years ago by 13k • written 7.9 years ago by ▴ 10
2
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1
reply
1.6k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.1 years ago by 40k • written 8.1 years ago by • 0
1
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2
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1.7k
views
Normalization factors in metagenomeSeq
microbiome
8.5 years ago jovel_juan ▴ 10
2
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4
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2.0k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 9 months ago by • 0 • written 8.6 years ago by ▴ 30
1
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1
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2.8k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by ▴ 30
1
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1
reply
1.4k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by ▴ 10
2
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2
replies
1.1k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
8.7 years ago noelle.noyes ▴ 30
2
votes
2
replies
1.4k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
8.7 years ago noelle.noyes ▴ 30
50 results • Page 1 of 1
Recent ...
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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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