Showing : microbiome • reset
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81
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 2 days ago by • 0 • written 4 days ago by • 0
0
votes
2
replies
398
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
4 months ago Elif • 0
1
vote
0
replies
163
views
News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
5 months ago Levi Waldron 1.1k
1
vote
3
replies
4.8k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 8 months ago by ▴ 30 • written 2.6 years ago by • 0
0
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1
reply
270
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 8 months ago by 63k • written 8 months ago by • 0
0
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3
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716
views
I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 10 months ago by 660 • written 10 months ago by • 0
1
vote
1
reply
751
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 13 months ago by 40k • written 13 months ago by • 0
0
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1
reply
471
views
DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 16 months ago by 40k • written 16 months ago by • 0
0
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1
reply
346
views
pairwise within sample
DESeq2 microbiome
updated 21 months ago by 40k • written 21 months ago by • 0
0
votes
1
reply
548
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 22 months ago by 63k • written 22 months ago by • 0
0
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1
reply
539
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 23 months ago by 3.8k • written 23 months ago by • 0
0
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0
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579
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
23 months ago GlycineMax • 0
0
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0
replies
676
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
2.3 years ago Matthew Ritchie ▴ 1000
0
votes
2
replies
796
views
Question: export edgeR normalised OTU table
microbiome edgeR
2.4 years ago Pozdrawiam • 0
0
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2
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1.1k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 2.7 years ago by 40k • written 2.7 years ago by • 0
0
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1
reply
965
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 3.2 years ago by • 0 • written 6.5 years ago by • 0
0
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2
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505
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 3.4 years ago by 40k • written 3.4 years ago by • 0
0
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0
replies
651
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
3.4 years ago lhuang7 ▴ 50
1
vote
0
replies
596
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
3.7 years ago supindab ▴ 10
0
votes
2
replies
887
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
3.9 years ago zhigang.li • 0
0
votes
2
replies
979
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 4.0 years ago by ★ 1.2k • written 4.0 years ago by • 0
0
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0
replies
632
views
Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
4.5 years ago mstagliamonte • 0
0
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1
reply
818
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
4.5 years ago slizo001 • 0
2
votes
1
reply
781
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 4.6 years ago by ★ 3.5k • written 4.6 years ago by ▴ 840
0
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1
reply
693
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 4.6 years ago by 40k • written 4.6 years ago by • 0
0
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1
reply
1.3k
views
DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 5.1 years ago by 40k • written 5.1 years ago by • 0
0
votes
0
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901
views
Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
5.2 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
903
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
5.3 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.1k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 5.5 years ago by 40k • written 5.5 years ago by • 0
1
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1
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1.3k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 5.6 years ago by ▴ 280 • written 5.6 years ago by ▴ 10
3
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2
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2.6k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 5.8 years ago by 40k • written 5.8 years ago by • 0
0
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6
replies
1.2k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
6.0 years ago lanhuong ▴ 20
0
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3
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1.3k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 6.2 years ago by 13k • written 6.2 years ago by • 0
1
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1
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2.9k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
6.2 years ago stats134711 • 0
0
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2
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1.2k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
6.5 years ago Brian Smith ▴ 120
6
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1
reply
2.5k
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 6.7 years ago by 13k • written 6.7 years ago by ▴ 20
0
votes
5
replies
3.1k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 6.8 years ago by ▴ 280 • written 6.8 years ago by • 0
0
votes
8
replies
2.8k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 6.8 years ago by 13k • written 9.5 years ago by 40k
0
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0
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1.0k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
6.8 years ago Daniel Brewer ▴ 90
4
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3
replies
1.6k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 6.9 years ago by 40k • written 6.9 years ago by • 0
0
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5
replies
1.2k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 7.6 years ago by 13k • written 7.6 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 7.7 years ago by 40k • written 7.7 years ago by • 0
1
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2
replies
1.6k
views
Normalization factors in metagenomeSeq
microbiome
8.2 years ago jovel_juan ▴ 10
2
votes
4
replies
1.8k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 5 months ago by • 0 • written 8.3 years ago by ▴ 30
1
vote
1
reply
2.6k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by ▴ 30
1
vote
1
reply
1.3k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by ▴ 10
2
votes
2
replies
1.0k
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
8.4 years ago noelle.noyes ▴ 30
2
votes
2
replies
1.3k
views
error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
8.4 years ago noelle.noyes ▴ 30
1
vote
1
reply
1.4k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by ▴ 30
0
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1
reply
1.1k
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
50 results • Page 1 of 1
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Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file by jenniferbrowngates • 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
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Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
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