Showing : Microbiome • reset
2
votes
19
replies
1.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 8.2 years ago by 37k • written 8.2 years ago by ▴ 130
0
votes
8
replies
2.5k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 5.9 years ago by 13k • written 8.6 years ago by 37k
0
votes
3
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 8.1 years ago by ▴ 130 • written 8.1 years ago by 37k
1
vote
2
replies
1.4k
views
Normalization factors in metagenomeSeq
microbiome
7.2 years ago jovel_juan ▴ 10
2
votes
2
replies
821
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
7.5 years ago • updated 7.4 years ago noelle.noyes ▴ 30
2
votes
2
replies
1.1k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
7.5 years ago noelle.noyes ▴ 30
4
votes
3
replies
1.3k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 6.0 years ago by 37k • written 6.0 years ago by • 0
0
votes
5
replies
2.6k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by • 0
0
votes
2
replies
538
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
3.0 years ago zhigang.li • 0
2
votes
3
replies
1.5k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 7.4 years ago by ▴ 280 • written 7.4 years ago by ▴ 30
0
votes
2
replies
986
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
5.6 years ago Brian Smith ▴ 120
1
vote
2
replies
4.1k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 7.7 years ago by 37k • written 7.7 years ago by • 0
0
votes
3
replies
1.0k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 5.2 years ago by 13k • written 5.2 years ago by • 0
3
votes
1
reply
1.8k
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 5.7 years ago by 13k • written 5.7 years ago by • 0
0
votes
1
reply
755
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 2.2 years ago by • 0 • written 5.5 years ago by • 0
0
votes
6
replies
983
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
5.0 years ago lanhuong ▴ 20
2
votes
2
replies
2.0k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 4.8 years ago by 37k • written 4.8 years ago by • 0
1
vote
1
reply
955
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 4.6 years ago by ▴ 280 • written 4.6 years ago by ▴ 10
1
vote
1
reply
830
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 4.6 years ago by 37k • written 4.6 years ago by • 0
0
votes
1
reply
922
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 4.1 years ago by 37k • written 4.1 years ago by • 0
0
votes
1
reply
487
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 3.6 years ago by 37k • written 3.6 years ago by • 0
2
votes
1
reply
570
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 3.6 years ago by ★ 3.4k • written 3.6 years ago by ▴ 840
0
votes
2
replies
600
views
DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 3.0 years ago by ★ 1.1k • written 3.0 years ago by • 0
0
votes
1
reply
898
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by • 0
1
vote
1
reply
1.3k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by ▴ 30
0
votes
2
replies
289
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 2.4 years ago by 37k • written 2.4 years ago by • 0
0
votes
2
replies
676
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 21 months ago by 37k • written 21 months ago by • 0
1
vote
2
replies
2.2k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
20 months ago Daniel • 0
1
vote
1
reply
1.1k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 7.4 years ago by ▴ 280 • written 7.4 years ago by ▴ 10
1
vote
1
reply
150
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 9 weeks ago by 37k • written 9 weeks ago by • 0
1
vote
1
reply
2.3k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 7.4 years ago by ▴ 280 • written 7.4 years ago by ▴ 30
0
votes
1
reply
211
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 5 months ago by 37k • written 5 months ago by • 0
0
votes
1
reply
167
views
pairwise within sample
DESeq2 microbiome
updated 10 months ago by 37k • written 10 months ago by • 0
2
votes
1
reply
1.4k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 6.8 years ago by 37k • written 6.8 years ago by • 0
0
votes
5
replies
1.0k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 6.6 years ago by 13k • written 6.6 years ago by ▴ 10
0
votes
3
replies
926
views
Correlation analysis
Microbiome HIV Microbiome HIV
updated 10.6 years ago by 21k • written 10.6 years ago by ▴ 20
0
votes
0
replies
288
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
12 months ago GlycineMax • 0
0
votes
0
replies
2.6k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
9.7 years ago Dan Tenenbaum ★ 8.2k
0
votes
0
replies
2.2k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
8.9 years ago Luo Weijun ★ 1.5k
0
votes
0
replies
857
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
5.9 years ago Daniel Brewer ▴ 90
1
vote
1
reply
2.3k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
5.2 years ago stats134711 • 0
0
votes
0
replies
699
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
4.4 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
683
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
4.2 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
543
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
3.5 years ago slizo001 • 0
0
votes
0
replies
428
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
3.5 years ago mstagliamonte • 0
1
vote
0
replies
389
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
2.7 years ago supindab ▴ 10
0
votes
0
replies
426
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
2.5 years ago lhuang7 ▴ 50
0
votes
2
replies
483
views
Question: export edgeR normalised OTU table
microbiome edgeR
17 months ago Pozdrawiam • 0
0
votes
0
replies
417
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
16 months ago Matthew Ritchie ▴ 1000
0
votes
1
reply
227
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 11 months ago by 60k • written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: miRNA differential expression analysis - treat as transcript level? by Michael Love 37k
This is very low and I think you can just use regular count-based methods safely. If you look at the ~3 features above 1 those are probably…
Comment: LogFC: how do you determine the cutoff for differentially expressed genes? by OE • 0
Hi Aaron, I have been performing some Diffrential Methylation Analysis and found some logFC values really closer to 0 ( from - 0.07 to 0.1…
Comment: Macbook M1 install genefilter failed by matt.broerman • 0
This error is similar to this one: https://stackoverflow.com/questions/66817276/how-to-install-rcpparmadillo-on-apple-silicon-m1-macs So i…
Comment: miRNA differential expression analysis - treat as transcript level? by BG • 0
Hi, attached is the plot for the inferential variance (code according to the fishpond vignette). How does this look to you? The first plot …
Answer: miRNA differential expression analysis - treat as transcript level? by Michael Love 37k
If it's "ok" depends on the amount of inferential uncertainty. We have benchmarked typical gene-level methods and found that we don't gain …
Votes
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
Answer: Help with limma contrast, difference of a difference?
Answer: Help with limma contrast, difference of a difference?
Answer: Help with limma contrast, difference of a difference?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Awards • All
Teacher to Michael Love 37k
Popular Question to Gordon Smyth 45k
Scholar to James W. MacDonald 60k
Popular Question to Nik Tuzov ▴ 70
Teacher to Kevin Blighe 3.5k
Locations • All
United States, 22 minutes ago
The city by the bay, 47 minutes ago
Switzerland, 2 hours ago
United States, 2 hours ago
United States, 2 hours ago
Traffic: 230 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