Showing : metagenomeseq • reset
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
12 days ago edissepo • 0
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0
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79
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
6 weeks ago GlycineMax • 0
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0
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87
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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
5 months ago Laura • 0
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0
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112
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
7 months ago Andrew • 0
0
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1
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623
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 16 months ago by • 0 • written 4.7 years ago by • 0
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0
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180
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Including covariates with fitFeatureModel
metagenomeSeq
21 months ago dkorandla • 0
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10
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609
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Phyloseq to metagenomeSeq
limma metagenomeSeq
2.2 years ago nabiyogesh • 0
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1
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406
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
2.6 years ago slizo001 • 0
0
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1
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597
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
3.2 years ago jol.espinoz ▴ 40
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0
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441
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Paired Difference Analysis
metagenomeseq
3.5 years ago nhua • 0
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2
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441
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
3.5 years ago arguello.rguez • 0
1
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1
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488
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 3.5 years ago by ▴ 280 • written 3.5 years ago by • 0
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1
reply
437
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 3.5 years ago by ▴ 60 • written 3.6 years ago by • 0
1
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1
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697
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 3.7 years ago by ▴ 280 • written 3.7 years ago by ▴ 10
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2
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600
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
4.1 years ago chawonhe • 0
2
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6
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2.4k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
4.4 years ago • updated 4.3 years ago sasha • 0
0
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1
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584
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 4.4 years ago by ▴ 280 • written 4.4 years ago by ▴ 10
0
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1
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515
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 4.4 years ago by ▴ 280 • written 4.4 years ago by ▴ 10
0
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1
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585
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 4.4 years ago by 57k • written 4.4 years ago by • 0
0
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6
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906
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 4.5 years ago by ▴ 280 • written 4.5 years ago by • 0
0
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2
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731
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 4.6 years ago by ▴ 280 • written 4.6 years ago by • 0
0
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2
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840
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
4.7 years ago Brian Smith ▴ 120
1
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4
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669
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by • 0
0
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1
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551
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Understand fold changes
metagenomeseq
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by ▴ 860
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5
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1.3k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 4.9 years ago by • 0 • written 4.9 years ago by ▴ 30
0
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5
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2.1k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 4.9 years ago by ▴ 280 • written 4.9 years ago by • 0
2
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1
reply
856
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by • 0
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1
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490
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 5.0 years ago by ▴ 280 • written 5.0 years ago by • 0
1
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2
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696
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
5.1 years ago pjgalli2 • 0
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1
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1.2k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by • 0
0
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1
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507
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Aggregate By Taxonomy Error
metagenomeSeq
updated 5.2 years ago by ▴ 280 • written 5.2 years ago by • 0
0
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5
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947
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
5.2 years ago David ▴ 860
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3
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987
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by ▴ 20
1
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1
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702
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 5.4 years ago by ▴ 280 • written 5.4 years ago by • 0
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0
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858
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
5.4 years ago craemuletz • 0
0
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0
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560
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
5.4 years ago craemuletz • 0
3
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5
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1.5k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 5.5 years ago by ▴ 280 • written 5.5 years ago by • 0
0
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6
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1.7k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
5.7 years ago • updated 5.6 years ago David ▴ 860
1
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1
reply
684
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metagenomeSeq - normFactors
metagenomeseq
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 120
1
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4
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983
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by • 0
4
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6
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747
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MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 6.1 years ago by 57k • written 6.1 years ago by • 0
0
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7
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1.1k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
1
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1
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675
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Metagenomeseq package; time series analysis
metagenomeseq software error
updated 6.4 years ago by ▴ 280 • written 6.4 years ago by • 0
1
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1
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825
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Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
6.5 years ago eertel • 0
2
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3
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1.3k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 30
1
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1
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2.1k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 30
1
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1
reply
956
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
2
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2
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720
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no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
6.6 years ago noelle.noyes ▴ 30
2
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2
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908
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error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
6.6 years ago noelle.noyes ▴ 30
2
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1
reply
1.5k
views
metagenomeSeq error using cumNormStatFast
metagenomeSeq
updated 6.6 years ago by ▴ 280 • written 6.6 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: error message from oligo package by Jesús • 0
Hola chchen. Actualmente estoy trabajando con Oligo y estoy tratando de aplicar MAS de la siguiente forma: backgroundCorrect (data, method…
Answer: Is there anyway to replace seqlevels in a txdb by James W. MacDonald 57k
``` > txdb <- makeTxDbFromBiomart(dataset = "mochrogaster_gene_ensembl") Download and preprocess the 'transcripts' data frame ... OK Dow…
Answer: extract the "start" position of matchPattern() by shepherl 2.8k
Average of start values: ``` > temp = matchPattern("A", "ACGTA", max.mismatch=0) > vls = start(temp) > mean(vls) ``` You will have to loo…
Answer: Paired samples analysis by Michael Love 33k
For questions about how to choose and interpret an appropriate statistical design, I would recommend working with a local statistician or s…
Comment: AlignmentsTrack empty plot by karlaarz • 0
No, it was my mistake while copying the script, but the output is still the same. I've already edited the post by removing the negative sym…
Votes
Comment: Compilation fatal error: iostream.h: No such file or directory when installing R
Answer: tximeta countsFromAbundance for downstream analysis
A: plotPCA - how to add labels to a PCA plot
A: plotPCA - how to add labels to a PCA plot
Answer: Can't produce a generegiontrack from my txdb anymore
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