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Showing :
metagenomeSeq
•
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0
votes
0
replies
356
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics
metagenomeSeq
microbiome
phyloseq
microbiomeDataSets
8 months ago
Mohamed
▴ 30
0
votes
1
reply
818
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
Aditya
• 0
0
votes
0
replies
632
views
Using MetagenomeSeq with intercept gives high logFC
limma
metagenomeSeq
2.8 years ago
edissepo
• 0
0
votes
0
replies
952
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq
Metagenomics
microbiome
microbiomeExplorer
2.8 years ago
GlycineMax
• 0
0
votes
0
replies
774
views
Problem with creating an MRexperiment with metagenomeseq - invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featu…
MRexperiment
metagenomes
metagenomeSeq
3.2 years ago
Laura
• 0
0
votes
0
replies
692
views
Fitzig function in MetagenomeSeq package
metagenomeSeq
fitzig
3.3 years ago
Andrew
• 0
0
votes
1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq
paired samples
microbiome
updated 4.1 years ago by
jananee15
• 0 • written 7.4 years ago by
marypadilha
• 0
0
votes
0
replies
890
views
Including covariates with fitFeatureModel
metagenomeSeq
4.5 years ago
dkorandla
• 0
0
votes
10
replies
1.9k
views
Phyloseq to metagenomeSeq
limma
metagenomeSeq
4.9 years ago
Jitendra
▴ 10
0
votes
1
reply
1.1k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error
metagenomeseq
microbiome
5.4 years ago
slizo001
• 0
0
votes
1
reply
1.4k
views
[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq
cumNormStatFast
features
error
5.9 years ago
jol.espinoz
▴ 40
0
votes
0
replies
968
views
Paired Difference Analysis
metagenomeseq
6.2 years ago
nhua
• 0
0
votes
2
replies
1.1k
views
Filter low counts OTUs from a MRfull table to prepare a heatmap
metagenomeseq
6.2 years ago
arguello.rguez
• 0
1
vote
1
reply
1.1k
views
Including taxa names in heatmap in metagenomeseq
gut microbiome
heatmap
metagenomeseq
updated 6.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.3 years ago by
arguello.rguez
• 0
0
votes
1
reply
994
views
metagenomeSeq pre-analysis Data Preporation for full genome sequencing
metagenomeSeq
full genome sequencing
updated 6.3 years ago by
Hector Corrada Bravo
▴ 60 • written 6.3 years ago by
cmapoulton
• 0
1
vote
1
reply
1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq
microbiome
gut microbiome
metagenomics
shotgun metagenomics
updated 6.4 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 6.4 years ago by
lilianeconteville
▴ 10
0
votes
2
replies
1.3k
views
How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq
plotmrheatmap
color key
6.8 years ago
chawonhe
• 0
2
votes
6
replies
4.1k
views
Difference between fitFeatureModel and fitZIG in metagenomeSeq
metagenomeseq
7.1 years ago
sasha
• 0
0
votes
1
reply
1.1k
views
metagenomeSeq: role for fitLogNormal?
metagenomeseq
updated 7.1 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.1 years ago by
handibles
▴ 10
0
votes
2
replies
1.1k
views
metagenomeSeq 1.16.0: unique features give NA's for logFC / p-val?
metagenomeseq
updated 4 months ago by
liqiong464
• 0 • written 7.1 years ago by
handibles
▴ 10
0
votes
1
reply
1.2k
views
Is it possible to create a Metagenomeseq heatmap with two coloured bars on the top?
metagenomeseq
heatmap
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
Key
• 0
0
votes
6
replies
1.8k
views
metagenomeSeq log transformation
metagenomeseq
logtransformation
updated 7.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.3 years ago by
PJ
• 0
0
votes
2
replies
1.4k
views
MetagenomeSeq: Sorting by sample type in plotMRheatmap
metagenomeSeq
plotMRheatmap
updated 7.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.3 years ago by
Rachael
• 0
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq
microbiome
7.4 years ago
Brian Smith
▴ 120
1
vote
4
replies
1.4k
views
error using fitTimeSeries in metagenomeSeq
metagenomeseq
fittimeseries
updated 7.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.5 years ago by
wijera81
• 0
0
votes
1
reply
1.0k
views
Understand fold changes
metagenomeseq
updated 7.6 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.6 years ago by
David
▴ 860
0
votes
6
replies
2.5k
views
paired analysis using metagenomeSeq
metagenomeseq
logfc
paired samples
standard error
updated 21 months ago by
tom830979
• 0 • written 7.6 years ago by
manasishah86
▴ 30
0
votes
5
replies
3.5k
views
DESeq2 16s microbiome size factors
deseq2
metagenomeseq
rnaseq
16s
microbiome
updated 7.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.7 years ago by
jbatsx
• 0
2
votes
1
reply
1.6k
views
Metagenome seq errors using biom (1.3) file
metagenomeseq
qiime
biom
updated 7.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.7 years ago by
dr.richrodrigues
• 0
0
votes
1
reply
918
views
fitTimeSeries possible error
metagenomeseq
fittimeseries
updated 7.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.7 years ago by
giulia.masetti
• 0
1
vote
2
replies
1.4k
views
metagenomeSeq for continuous phenotype
metagenomeseq
continuous
limma
7.8 years ago
pjgalli2
• 0
0
votes
1
reply
1.7k
views
fitZig coefficient for interaction terms?
metagenomeseq
updated 7.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.9 years ago by
nhuda6
• 0
0
votes
1
reply
1.0k
views
Aggregate By Taxonomy Error
metagenomeSeq
updated 7.9 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 7.9 years ago by
nhuda6
• 0
0
votes
5
replies
1.8k
views
MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq
anova
metagenomics
8.0 years ago
David
▴ 860
0
votes
3
replies
1.6k
views
Normalisation problem in metagenomeSeq
normalization
metagenomeseq
updated 8.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.0 years ago by
Stephen Rolfe
▴ 20
1
vote
1
reply
1.2k
views
Multiple variables in fitFeaturemodel
metagenomeseq
updated 8.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.2 years ago by
sajancr
• 0
0
votes
0
replies
1.4k
views
Dramatically different results from comparing multiple groups using fitZig versus fitFeatureModel
metagenomeseq
8.2 years ago
craemuletz
• 0
0
votes
0
replies
983
views
Differential abundance for elevational gradient survey -- use fitTimeSeries?
metagenomeseq
8.2 years ago
craemuletz
• 0
3
votes
5
replies
2.5k
views
Interpretation for MRfulltable of fitzig in Metagenomeseq
metagenomeseq
fitzig
MRfulltable
updated 8.2 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.2 years ago by
Han-Na Kim
• 0
0
votes
6
replies
3.2k
views
Alpha diversity on Rlogtransformed data
deseq2
phyloseq
metagenomeseq
8.4 years ago
David
▴ 860
1
vote
1
reply
1.2k
views
metagenomeSeq - normFactors
metagenomeseq
updated 8.5 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.5 years ago by
Brian Smith
▴ 120
1
vote
4
replies
1.7k
views
creating a subsetted MRexperiment based on sample name?
metagenomeseq
updated 8.7 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 8.7 years ago by
rleonzay
• 0
4
votes
6
replies
1.5k
views
MetagenomeSeq sparsefeature question
metagenomeseq
sparsefeature
cumnorm
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
yang.xiang1030
• 0
0
votes
7
replies
1.9k
views
metagenomeSeq cumNorm issue with NAs in real data
metagenomeseq
updated 9.0 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.0 years ago by
carr0603
• 0
1
vote
1
reply
1.2k
views
Metagenomeseq package; time series analysis
metagenomeseq
software error
updated 9.1 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.1 years ago by
pvp2101
• 0
1
vote
1
reply
1.4k
views
Omission of final edge in correlationTest
metagenomeseq error
correlationTest
metagenomeseq
9.2 years ago
eertel
• 0
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq
microbiome
updated 16 months ago by
Muhammad
• 0 • written 9.2 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq
microbiome
updated 9.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.3 years ago by
noelle.noyes
▴ 30
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome
microbiome
metagenomeseq
updated 9.3 years ago by
Joseph Nathaniel Paulson
▴ 280 • written 9.3 years ago by
jovel_juan
▴ 30
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq
fitTimeSeries
microbiome
9.3 years ago
noelle.noyes
▴ 30
50 results • Page
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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