Showing : Microbiome • reset
0
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1
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73
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pairwise within sample
DESeq2 microbiome
updated 25 days ago by 34k • written 27 days ago by • 0
0
votes
1
reply
99
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 8 weeks ago by 58k • written 8 weeks ago by • 0
0
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1
reply
128
views
Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 12 weeks ago by 3.4k • written 12 weeks ago by • 0
0
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0
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111
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
3 months ago GlycineMax • 0
0
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0
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221
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News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
7 months ago Matthew Ritchie ▴ 1000
0
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2
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284
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Question: export edgeR normalised OTU table
microbiome edgeR
7 months ago Pozdrawiam • 0
1
vote
2
replies
947
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
11 months ago Daniel • 0
0
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2
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305
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 12 months ago by 34k • written 12 months ago by • 0
0
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1
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654
views
MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 17 months ago by • 0 • written 4.8 years ago by • 0
0
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2
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182
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 20 months ago by 34k • written 20 months ago by • 0
0
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0
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282
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
20 months ago lhuang7 ▴ 50
1
vote
0
replies
280
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
23 months ago supindab ▴ 10
0
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2
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380
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
2.2 years ago zhigang.li • 0
0
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2
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251
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 2.3 years ago by ▴ 850 • written 2.3 years ago by • 0
0
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0
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311
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Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
2.8 years ago mstagliamonte • 0
0
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1
reply
430
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
2.8 years ago slizo001 • 0
2
votes
1
reply
430
views
Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 2.9 years ago by ★ 3.3k • written 2.9 years ago by ▴ 840
0
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1
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382
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 2.9 years ago by 34k • written 2.9 years ago by • 0
0
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1
reply
513
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DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 3.4 years ago by 34k • written 3.4 years ago by • 0
0
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0
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561
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Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
3.5 years ago Jenny Drnevich ★ 2.0k
0
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0
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577
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
3.6 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
693
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 3.8 years ago by 34k • written 3.8 years ago by • 0
1
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1
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739
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 3.8 years ago by ▴ 280 • written 3.9 years ago by ▴ 10
2
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2
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1.6k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 4.0 years ago by 34k • written 4.0 years ago by • 0
0
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6
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852
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Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
4.3 years ago lanhuong ▴ 20
0
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3
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895
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 4.4 years ago by 13k • written 4.4 years ago by • 0
1
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1
reply
1.9k
views
Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
4.5 years ago • updated 4.4 years ago stats134711 • 0
0
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2
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870
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
4.8 years ago Brian Smith ▴ 120
2
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1
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1.4k
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 5.0 years ago by 13k • written 5.0 years ago by • 0
0
votes
5
replies
2.2k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 5.1 years ago by ▴ 280 • written 5.1 years ago by • 0
0
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8
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2.3k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 5.1 years ago by 13k • written 7.8 years ago by 34k
0
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769
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Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
5.1 years ago Daniel Brewer ▴ 90
4
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3
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1.1k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 5.2 years ago by 34k • written 5.2 years ago by • 0
0
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5
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925
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 5.9 years ago by 13k • written 5.9 years ago by ▴ 10
2
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1
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1.3k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 6.0 years ago by 34k • written 6.0 years ago by • 0
1
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2
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1.3k
views
Normalization factors in metagenomeSeq
microbiome
6.4 years ago jovel_juan ▴ 10
2
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3
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1.4k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 6.6 years ago by ▴ 280 • written 6.6 years ago by ▴ 30
1
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1
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2.1k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 6.7 years ago by ▴ 280 • written 6.7 years ago by ▴ 30
1
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1
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981
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Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 6.7 years ago by ▴ 280 • written 6.7 years ago by ▴ 10
2
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2
replies
739
views
no timeInterval output using fitTimeSeries
metagenomeSeq fitTimeSeries microbiome
6.7 years ago noelle.noyes ▴ 30
2
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2
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938
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error using fitTimeSeries from metagenomeSeq
metagenomeSeq microbiome
6.7 years ago noelle.noyes ▴ 30
1
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1
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1.2k
views
metagenomeSeq error using plotMRheatmap and display() heatmaps and PCA/MDS plots
metagenomseq microbiome
updated 6.7 years ago by ▴ 280 • written 6.7 years ago by ▴ 30
0
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1
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819
views
error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
microbiome
updated 6.9 years ago by ▴ 280 • written 6.9 years ago by • 0
1
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2
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4.0k
views
DESeq2: What is the impact if glm.fit does not converge during rlogTransformation or varianceStabilizingTransformation
deseq2 normalization microbiome
updated 7.0 years ago by 34k • written 7.0 years ago by • 0
0
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3
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2.7k
views
phyloseq/DESeq gives negative transformed values
Microbiome Normalization Clustering DESeq DESeq2 Microbiome Normalization Clustering DESeq
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by 34k
2
votes
19
replies
1.6k
views
phyloseq/DESeq gives negative transformed values
Microbiome DESeq Microbiome DESeq
updated 7.4 years ago by 34k • written 7.5 years ago by ▴ 130
0
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0
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2.1k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
8.2 years ago Luo Weijun ★ 1.5k
0
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0
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2.4k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
9.0 years ago Dan Tenenbaum ★ 8.2k
0
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3
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813
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Correlation analysis
Microbiome HIV Microbiome HIV
updated 9.9 years ago by 21k • written 9.9 years ago by ▴ 20
49 results • Page 1 of 1
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Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Comment: "full model matrix is less than full rank" by fernandogs97 • 0
Hello ATpoint, thank you very much for your fast and helpful response, finally I corrected the error by changing the separator, instead of …
Comment: unable to load shared object Rsamtools.dll': by Mike Smith ★ 5.1k
Can you include the command you're running (I guess it's `BiocManager::install("Rsamtools", type = "source")` )? It would also be useful to…
Comment: unable to load shared object Rsamtools.dll': by franck.richard • 0
Finally, I only encounter this problem with Rsamtools. It works fine with the other packages. Thank you for your help!
Comment: Unique GPos taking into account mcols by maltethodberg ▴ 140
Yes, I managed to find those functions via the VariantAnnotation package. The "Quad" versions are very handy for matching seqnames/pos/effe…
Votes
Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
Comment: deseq2 machine sizing best practices for very large data set
Comment: Warning messages on Apple M1 BigSur
Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset
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