Showing : metagenomeseq • reset
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 5 months ago by • 0 • written 7.1 years ago by ▴ 10
0
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0
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382
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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
9 months ago Mohamed ▴ 30
2
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4
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2.3k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 17 months ago by • 0 • written 9.3 years ago by ▴ 30
0
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6
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2.5k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 22 months ago by • 0 • written 7.7 years ago by ▴ 30
0
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1
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847
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
0
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0
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652
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
2.8 years ago edissepo • 0
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0
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979
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
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0
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793
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Problem with creating an MRexperiment with metagenomeseq - invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featu…
MRexperiment metagenomes metagenomeSeq
3.3 years ago Laura • 0
0
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0
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711
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
3.4 years ago Andrew • 0
0
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1
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1.3k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.1 years ago by • 0 • written 7.4 years ago by • 0
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0
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912
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Including covariates with fitFeatureModel
metagenomeSeq
4.5 years ago dkorandla • 0
0
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10
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1.9k
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Phyloseq to metagenomeSeq
limma metagenomeSeq
5.0 years ago Jitendra ▴ 10
0
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1
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1.1k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.4 years ago slizo001 • 0
0
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1
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1.4k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
6.0 years ago jol.espinoz ▴ 40
0
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0
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982
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Paired Difference Analysis
metagenomeseq
6.3 years ago nhua • 0
0
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2
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1.2k
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.3 years ago arguello.rguez • 0
1
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1
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1.2k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
0
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1
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1.0k
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 6.3 years ago by ▴ 60 • written 6.3 years ago by • 0
1
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1
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1.8k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
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2
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1.3k
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
6.9 years ago chawonhe • 0
2
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6
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4.2k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.2 years ago • updated 7.1 years ago sasha • 0
0
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1
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1.1k
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by ▴ 10
0
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1
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1.2k
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 7.2 years ago by 65k • written 7.2 years ago by • 0
0
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6
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1.9k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by • 0
0
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2
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1.5k
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 7.4 years ago by ▴ 280 • written 7.4 years ago by • 0
0
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2
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1.5k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.5 years ago Brian Smith ▴ 120
1
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4
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1.4k
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by • 0
0
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1
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1.0k
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Understand fold changes
metagenomeseq
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 860
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5
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3.6k
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DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
2
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1
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1.6k
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by • 0
0
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1
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930
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by • 0
1
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2
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1.4k
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
7.9 years ago pjgalli2 • 0
0
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1
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1.7k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by • 0
0
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1
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1.1k
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Aggregate By Taxonomy Error
metagenomeSeq
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by • 0
0
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5
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1.8k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.0 years ago David ▴ 860
0
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3
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1.7k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 8.1 years ago by ▴ 280 • written 8.1 years ago by ▴ 20
1
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1
reply
1.2k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
0
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0
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1.4k
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
8.2 years ago craemuletz • 0
0
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0
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995
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.2 years ago craemuletz • 0
3
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5
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2.5k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by • 0
0
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6
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3.2k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
8.4 years ago David ▴ 860
1
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1
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1.2k
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metagenomeSeq - normFactors
metagenomeseq
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by ▴ 120
1
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4
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1.7k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by • 0
4
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6
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1.5k
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MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 8.9 years ago by 65k • written 8.9 years ago by • 0
0
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7
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2.0k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
1
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1
reply
1.2k
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Metagenomeseq package; time series analysis
metagenomeseq software error
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by • 0
1
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1
reply
1.4k
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Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
9.2 years ago eertel • 0
1
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1
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3.0k
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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
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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
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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: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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