Showing : microbiome • reset
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
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
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
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
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
2
votes
1
reply
1.6k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 24 months ago by 41k • written 24 months ago by ▴ 10
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
2
votes
1
reply
1.1k
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.4 years ago by ★ 3.6k • written 5.4 years ago by ▴ 850
2
votes
1
reply
966
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
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
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
1
vote
2
replies
1.9k
views
Normalization factors in metagenomeSeq
microbiome
9.0 years ago jovel_juan ▴ 30
1
vote
1
reply
3.5k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.0 years ago stats134711 • 0
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
1
vote
0
replies
492
views
News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
16 months ago Levi Waldron ★ 1.1k
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
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
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
0
replies
862
views
Job: Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job bioinformatician systems biology microbiome genomics Job
4.5 years ago supindab ▴ 10
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
0
votes
0
replies
924
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
4.3 years ago lhuang7 ▴ 50
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
666
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 6 days ago by • 0 • written 10 months ago by • 0
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
986
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
2
replies
462
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
5 months ago anton.kratz ▴ 60
0
votes
1
reply
877
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
0
votes
3
replies
1.6k
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 20 months ago by 690 • written 20 months ago by • 0
0
votes
1
reply
766
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
2
replies
1.3k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
14 months ago Elif • 0
0
votes
1
reply
561
views
pairwise within sample
DESeq2 microbiome
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
0
votes
1
reply
656
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
1
reply
847
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
940
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
votes
0
replies
351
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
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
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
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
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.5 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
2.6k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
10.7 years ago Luo Weijun ★ 1.6k
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
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
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
0
votes
0
replies
1.3k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
7.7 years ago Daniel Brewer ▴ 100
0
votes
2
replies
1.5k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.4 years ago Brian Smith ▴ 120
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Awards • All
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Popular Question to W. Evan Johnson ▴ 850
Popular Question to Alejandro Reyes ★ 1.9k
Locations • All
Germany, just now
EMBL Heidelberg, 5 minutes ago
WEHI, Melbourne, Australia, 6 minutes ago
Mexico, 13 minutes ago
China, 15 minutes ago
Traffic: 565 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6