Showing : metagenomeSeq • reset
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Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq cumulativesumscaling
updated 27 days ago by 68k • written 4 weeks ago by • 0
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678
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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
18 months ago Mohamed ▴ 30
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1
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1.1k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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915
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
3.6 years ago edissepo • 0
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1.3k
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3.7 years ago GlycineMax • 0
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993
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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
4.1 years ago Laura • 0
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945
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4.2 years ago Andrew • 0
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1
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1.5k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.9 years ago by • 0 • written 8.3 years ago by • 0
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0
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1.2k
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Including covariates with fitFeatureModel
metagenomeSeq
5.3 years ago dkorandla • 0
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10
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2.4k
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Phyloseq to metagenomeSeq
limma metagenomeSeq
5.8 years ago Jitendra ▴ 10
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1
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1.4k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
6.2 years ago slizo001 • 0
0
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1
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1.7k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
6.8 years ago jol.espinoz ▴ 40
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1.2k
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Paired Difference Analysis
metagenomeseq
7.1 years ago nhua • 0
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2
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1.5k
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
7.1 years ago arguello.rguez • 0
1
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1
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1.4k
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by • 0
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1
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1.2k
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 7.1 years ago by ▴ 60 • written 7.2 years ago by • 0
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1
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2.1k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 10
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2
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1.5k
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
7.7 years ago chawonhe • 0
2
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6
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4.8k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
8.0 years ago • updated 7.9 years ago sasha • 0
0
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1
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1.3k
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 8.0 years ago by ▴ 280 • written 8.0 years ago by ▴ 20
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2
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1.4k
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 15 months ago by • 0 • written 8.0 years ago by ▴ 20
0
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1
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1.5k
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
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6
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2.3k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 8.1 years ago by ▴ 280 • written 8.1 years ago by • 0
0
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2
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1.7k
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
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2
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1.8k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
8.3 years ago Brian Smith ▴ 120
1
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4
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1.7k
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
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1
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1.3k
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Understand fold changes
metagenomeseq
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by ▴ 860
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6
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2.9k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 2.6 years ago by • 0 • written 8.5 years ago by ▴ 30
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5
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3.9k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by • 0
2
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1
reply
1.9k
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
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1
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1.1k
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
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2
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1.6k
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
8.7 years ago pjgalli2 • 0
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1
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1.9k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by • 0
0
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1
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1.3k
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Aggregate By Taxonomy Error
metagenomeSeq
updated 8.8 years ago by ▴ 280 • written 8.8 years ago by • 0
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5
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2.2k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.8 years ago David ▴ 860
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3
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1.9k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ▴ 20
1
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1
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1.4k
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 9.0 years ago by ▴ 280 • written 9.0 years ago by • 0
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0
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1.6k
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
9.0 years ago craemuletz • 0
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0
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1.2k
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
9.0 years ago craemuletz • 0
3
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5
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2.9k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by • 0
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6
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3.7k
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Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
9.3 years ago • updated 9.2 years ago David ▴ 860
1
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1
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1.4k
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metagenomeSeq - normFactors
metagenomeseq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 120
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4
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2.0k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 9.6 years ago by ▴ 280 • written 9.6 years ago by • 0
4
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6
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1.8k
views
MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 9.7 years ago by 68k • written 9.7 years ago by • 0
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7
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2.4k
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metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.9 years ago by ▴ 280 • written 9.9 years ago by • 0
1
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1
reply
1.4k
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 10.0 years ago by ▴ 280 • written 10.0 years ago by • 0
1
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1
reply
1.6k
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Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
10.1 years ago eertel • 0
2
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4
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2.7k
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normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 2.2 years ago by • 0 • written 10.1 years ago by ▴ 30
1
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1
reply
3.4k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ▴ 30
1
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1
reply
1.8k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Hoover • 0
I got it! ([Drift Boss][1]) [1]: https://driftbossgame.co
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Answer: Differential expression of proteins using somascan data
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Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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