Showing : metagenomeseq • reset
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 5 weeks ago by 36k • written 5 weeks ago by • 0
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0
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180
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Using MetagenomeSeq with intercept gives high logFC
limma metagenomeSeq
9 months ago edissepo • 0
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0
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261
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
11 months ago GlycineMax • 0
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0
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224
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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
15 months ago Laura • 0
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0
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260
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Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
16 months ago Andrew • 0
0
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1
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741
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 2.1 years ago by • 0 • written 5.4 years ago by • 0
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0
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336
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Including covariates with fitFeatureModel
metagenomeSeq
2.5 years ago dkorandla • 0
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10
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882
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Phyloseq to metagenomeSeq
limma metagenomeSeq
3.0 years ago nabiyogesh ▴ 10
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1
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527
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
3.4 years ago slizo001 • 0
0
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1
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751
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
4.0 years ago jol.espinoz ▴ 40
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0
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551
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Paired Difference Analysis
metagenomeseq
4.3 years ago nhua • 0
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2
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582
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Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
4.3 years ago arguello.rguez • 0
1
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1
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626
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Including taxa names in heatmap in metagenomeseq
gut microbiome heatmap metagenomeseq
updated 4.3 years ago by ▴ 280 • written 4.3 years ago by • 0
0
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1
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540
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metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq full genome sequencing
updated 4.3 years ago by ▴ 60 • written 4.3 years ago by • 0
1
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1
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914
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 4.5 years ago by ▴ 280 • written 4.5 years ago by ▴ 10
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2
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749
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How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq plotmrheatmap color key
4.9 years ago chawonhe • 0
2
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6
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2.9k
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Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
5.2 years ago • updated 5.1 years ago sasha • 0
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1
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677
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metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 5.1 years ago by ▴ 280 • written 5.1 years ago by ▴ 10
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1
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599
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metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 5.1 years ago by ▴ 280 • written 5.1 years ago by ▴ 10
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1
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669
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Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq heatmap
updated 5.2 years ago by 59k • written 5.2 years ago by • 0
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6
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1.1k
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metagenomeSeq log transformation
metagenomeseq logtransformation
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by • 0
0
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2
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898
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MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq plotMRheatmap
updated 5.4 years ago by ▴ 280 • written 5.4 years ago by • 0
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2
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963
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
5.5 years ago Brian Smith ▴ 120
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4
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796
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error using fitTimeSeries in metagenomeSeq
metagenomeseq fittimeseries
updated 5.6 years ago by ▴ 280 • written 5.6 years ago by • 0
0
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1
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635
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Understand fold changes
metagenomeseq
updated 5.6 years ago by ▴ 280 • written 5.6 years ago by ▴ 860
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5
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1.5k
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paired analysis using metagenomeSeq
metagenomeseq logfc paired samples standard error
updated 5.7 years ago by • 0 • written 5.7 years ago by ▴ 30
0
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5
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2.6k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by • 0
2
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1
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1.0k
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Metagenome seq errors using biom (1.3) file
metagenomeseq qiime biom
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by • 0
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1
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578
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fitTimeSeries possible error
metagenomeseq fittimeseries
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by • 0
1
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2
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859
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metagenomeSeq for continuous phenotype
metagenomeseq continuous limma
5.9 years ago pjgalli2 • 0
0
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1
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1.3k
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fitZig coefficient for interaction terms?
metagenomeseq
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by • 0
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1
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608
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Aggregate By Taxonomy Error
metagenomeSeq
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by • 0
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5
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1.1k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
6.0 years ago David ▴ 860
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3
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1.1k
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Normalisation problem in metagenomeSeq
normalization metagenomeseq
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by ▴ 20
1
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1
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827
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Multiple variables in fitFeaturemodel
metagenomeseq
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by • 0
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0
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954
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Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
6.2 years ago craemuletz • 0
0
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0
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640
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Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
6.2 years ago craemuletz • 0
3
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5
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1.8k
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Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq fitzig MRfulltable
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by • 0
0
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6
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2.2k
views
Alpha diversity on Rlogtransformed data
deseq2 phyloseq metagenomeseq
6.4 years ago David ▴ 860
1
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1
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780
views
metagenomeSeq - normFactors
metagenomeseq
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 120
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4
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1.1k
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creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 6.8 years ago by ▴ 280 • written 6.8 years ago by • 0
4
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6
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900
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MetagenomeSeq sparsefeature question
metagenomeseq sparsefeature cumnorm
updated 6.9 years ago by 59k • written 6.9 years ago by • 0
0
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7
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1.2k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 7.1 years ago by ▴ 280 • written 7.1 years ago by • 0
1
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1
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755
views
Metagenomeseq package; time series analysis
metagenomeseq software error
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by • 0
1
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1
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948
views
Omission of final edge in correlationTest
metagenomeseq error correlationTest metagenomeseq
7.2 years ago eertel • 0
2
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3
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1.5k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 30
1
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1
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2.2k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 30
1
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1
reply
1.1k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 7.3 years ago by ▴ 280 • written 7.3 years ago by ▴ 10
2
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2
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812
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no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
7.3 years ago noelle.noyes ▴ 30
2
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2
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1.1k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
7.3 years ago noelle.noyes ▴ 30
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Comment: EnrichGO not working with db created from annotationhub by Lucía • 0
I have this, can this be used for GO in R? ``` 115709282 LOC115709282 phenylalanine ammonia-lyase 115699364 LOC115699364 …
Answer: EnrichGO not working with db created from annotationhub by Lucía • 0
Hi, thanks so much for all your replies and running the code and confirming. I have not seen any GO term annotations for Cannabis so far…
Comment: TPM data Differential expression analysis by Gordon Smyth 45k
I have nothing to add my previous answer, which seems quite clear and umbiguous.
Answer: Difference between raw counts and featureCounts for DESeq2 by swbarnes2 ★ 1.0k
The count output from featureCounts is suitable for use with DESeq.
Comment: Subsetting operation on CompressedGRangesList object 'x' produces a result tha by Jiping Wang ▴ 70
Hi H. Do you have any clues what the bug or problem could be? thanks. Jiping
Votes
Answer: Difference between raw counts and featureCounts for DESeq2
Comment: Case Studies Data Missing in Rsubread
Answer: rtracklayer S.h
Answer: rtracklayer S.h
Answer: DESeq2: Extracting Averaged Counts Information from dds and rld
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