Showing : Microbiome • reset
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 10.0 years ago by 41k • written 10.0 years ago by ▴ 130
0
votes
8
replies
3.2k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.7 years ago by ★ 13k • written 10.4 years ago by 41k
0
votes
3
replies
3.3k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 10.0 years ago by ▴ 130 • written 10.0 years ago by 41k
4
votes
3
replies
2.0k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 7.8 years ago by 41k • written 7.8 years ago by • 0
0
votes
5
replies
3.5k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by • 0
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.4 years ago Brian Smith ▴ 120
0
votes
3
replies
1.6k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
2
votes
2
replies
1.5k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
9.3 years ago noelle.noyes ▴ 30
2
votes
2
replies
1.3k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
9.3 years ago noelle.noyes ▴ 30
1
vote
3
replies
6.8k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 18 months ago by ▴ 30 • written 3.5 years ago by • 0
2
votes
4
replies
2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 16 months ago by • 0 • written 9.2 years ago by ▴ 30
0
votes
2
replies
1.3k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.8 years ago zhigang.li • 0
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.0 years ago jovel_juan ▴ 30
1
vote
2
replies
4.6k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 9.6 years ago by 41k • written 9.6 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 4.8 years ago by ★ 1.3k • written 4.8 years ago by • 0
0
votes
3
replies
1.4k
views
Correlation analysis
Microbiome HIV Microbiome HIV
updated 12.5 years ago by 21k • written 12.5 years ago by ▴ 20
0
votes
1
reply
1.2k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 9.4 years ago by ▴ 280 • written 9.5 years ago by • 0
1
vote
1
reply
1.7k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
vote
1
reply
1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 30
1
vote
1
reply
3.0k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 30
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.6 years ago by 41k • written 8.6 years ago by • 0
0
votes
5
replies
1.5k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 10
6
votes
1
reply
3.2k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma rna-seq multi-mapped reads normalization microbiome
updated 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 20
0
votes
1
reply
1.2k
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.0 years ago by • 0 • written 7.4 years ago by • 0
0
votes
6
replies
1.6k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
6.9 years ago lanhuong ▴ 20
3
votes
2
replies
3.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.6 years ago by 41k • written 6.6 years ago by • 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 ▴ 280 • written 6.4 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
0
votes
1
reply
1.6k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 850
0
votes
2
replies
826
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 4.2 years ago by 41k • written 4.2 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.6 years ago by 41k • written 3.6 years ago by • 0
0
votes
1
reply
671
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 7 days ago by • 0 • written 10 months ago by • 0
2
votes
1
reply
1.6k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.0 years ago by 41k • written 2.0 years ago by ▴ 10
0
votes
2
replies
463
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
5 months ago anton.kratz ▴ 60
0
votes
1
reply
767
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
votes
1
reply
563
views
pairwise within sample
DESeq2 microbiome
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
2
votes
1
reply
969
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 7 months ago by ★ 4.0k • written 7 months ago by ▴ 10
0
votes
1
reply
659
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 19 months ago by 65k • written 19 months ago by • 0
0
votes
0
replies
352
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
2
replies
1.3k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
14 months ago Elif • 0
0
votes
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.6 years ago Dan Tenenbaum ★ 8.2k
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.2 years ago Jenny Drnevich ★ 2.0k
1
vote
0
replies
493
views
News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
16 months ago Levi Waldron ★ 1.1k
0
votes
2
replies
1.2k
views
Question: export edgeR normalised OTU table
microbiome edgeR
3.2 years ago Pozdrawiam • 0
0
votes
0
replies
987
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
3.2 years ago Matthew Ritchie ▴ 1000
0
votes
1
reply
850
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
0
replies
1.3k
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
6.1 years ago Jenny Drnevich ★ 2.0k
50 results • Page 1 of 1
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia) by christianhilton64 • 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Scholar to Robert Castelo ★ 3.2k
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