Showing : metagenomeseq • reset
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Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq cumulativesumscaling
updated 10 months ago by 68k • written 10 months ago by • 0
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914
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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
2.3 years ago Mohamed ▴ 30
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1
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1.4k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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1.1k
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
4.4 years ago edissepo • 0
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1.5k
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
4.5 years ago GlycineMax • 0
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0
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1.1k
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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
4.8 years ago Laura • 0
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1.2k
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4.9 years ago Andrew • 0
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1
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1.7k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.7 years ago by • 0 • written 9.0 years ago by • 0
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1.5k
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Including covariates with fitFeatureModel
metagenomeSeq
6.1 years ago dkorandla • 0
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10
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2.9k
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Phyloseq to metagenomeSeq
limma metagenomeSeq
6.6 years ago Jitendra ▴ 10
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1
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1.6k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
7.0 years ago slizo001 • 0
0
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1
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1.9k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
7.6 years ago jol.espinoz ▴ 40
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1.4k
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Paired Difference Analysis
metagenomeseq
7.9 years ago nhua • 0
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2
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1.7k
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
7.9 years ago arguello.rguez • 0
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1
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1.6k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by • 0
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1
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1.5k
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 7.9 years ago by ▴ 60 • written 7.9 years ago by • 0
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1
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2.3k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 8.1 years ago by ▴ 280 • written 8.1 years ago by ▴ 10
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2
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1.7k
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
8.5 years ago chawonhe • 0
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6
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5.3k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
8.7 years ago sasha • 0
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1
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1.4k
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 8.7 years ago by ▴ 280 • written 8.7 years ago by ▴ 20
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2
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1.6k
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 2.0 years ago by • 0 • written 8.7 years ago by ▴ 20
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1
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1.6k
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
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6
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2.5k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by • 0
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2
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1.9k
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by • 0
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2
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1.9k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
9.1 years ago • updated 9.0 years ago Brian Smith ▴ 120
1
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4
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1.9k
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by • 0
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1
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1.5k
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Understand fold changes
metagenomeseq
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 860
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6
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3.2k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 3.4 years ago by • 0 • written 9.2 years ago by ▴ 30
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5
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4.4k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by • 0
2
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1
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2.0k
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by • 0
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1
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1.3k
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 9.4 years ago by ▴ 280 • written 9.4 years ago by • 0
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2
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1.8k
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
9.4 years ago pjgalli2 • 0
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1
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2.0k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by • 0
0
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1
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1.4k
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Aggregate By Taxonomy Error
metagenomeSeq
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by • 0
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5
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2.5k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
9.6 years ago David ▴ 860
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3
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2.2k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 9.7 years ago by ▴ 280 • written 9.7 years ago by ▴ 20
1
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1
reply
1.6k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 9.8 years ago by ▴ 280 • written 9.8 years ago by • 0
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0
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1.8k
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
9.8 years ago craemuletz • 0
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0
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1.3k
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
9.8 years ago craemuletz • 0
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5
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3.3k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 9.8 years ago by ▴ 280 • written 9.8 years ago by • 0
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6
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4.0k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
10.0 years ago David ▴ 860
1
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1
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1.5k
views
metagenomeSeq - normFactors
metagenomeseq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ▴ 120
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4
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2.3k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 10.4 years ago by ▴ 280 • written 10.4 years ago by • 0
4
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6
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2.0k
views
MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 10.4 years ago by 68k • written 10.4 years ago by • 0
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7
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2.7k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 10.7 years ago by ▴ 280 • written 10.7 years ago by • 0
1
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1
reply
1.6k
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 10.7 years ago by ▴ 280 • written 10.7 years ago by • 0
1
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1
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1.8k
views
Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
10.8 years ago eertel • 0
2
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4
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2.9k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 3.0 years ago by • 0 • written 10.8 years ago by ▴ 30
1
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1
reply
3.7k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.9 years ago by ▴ 280 • written 10.9 years ago by ▴ 30
1
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1
reply
2.0k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 10.9 years ago by ▴ 280 • written 10.9 years ago by ▴ 30
56 results • Page 1 of 2
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Comment: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP by TikTsoksocissalpc • 0
Normalizing complex datasets like Hi C can be challenging, much like setting up a PC for optimal gaming performance. Just as careful tuning…
Comment: p.adjust BH Question by TikTsoksocissalpc • 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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