Showing : microbiome • reset
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
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3
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1.8k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 17 months ago by • 0 • written 2.5 years ago by • 0
1
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1
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638
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 19 months ago by ▴ 40 • written 19 months ago by ★ 1.6k
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2
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1.4k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
2.1 years ago anton.kratz ▴ 60
2
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1
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2.4k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 10
0
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0
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911
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.3 years ago Mohamed ▴ 30
0
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2
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3.0k
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
2.8 years ago Elif • 0
1
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0
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971
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
3.0 years ago Levi Waldron ★ 1.1k
1
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3
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9.2k
views
DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 3.2 years ago by ▴ 40 • written 5.1 years ago by • 0
0
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1
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1.2k
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
0
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3
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2.7k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 3.3 years ago by 700 • written 3.3 years ago by • 0
2
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1
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2.8k
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
0
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1
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1.3k
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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1
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957
views
pairwise within sample
DESeq2 microbiome
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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1
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1.5k
views
Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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1
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1.4k
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Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
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0
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1.5k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
4.5 years ago GlycineMax • 0
0
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0
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1.5k
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News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
4.8 years ago Matthew Ritchie ▴ 1000
0
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2
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1.6k
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Question: export edgeR normalised OTU table
microbiome edgeR
4.9 years ago Pozdrawiam • 0
0
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2
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2.5k
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Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
0
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1
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1.7k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.7 years ago by • 0 • written 9.0 years ago by • 0
0
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2
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1.3k
views
DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
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0
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1.4k
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
5.9 years ago lhuang7 ▴ 50
1
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0
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1.3k
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
6.2 years ago supindab ▴ 10
0
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2
replies
1.9k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
6.4 years ago zhigang.li • 0
0
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2
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2.0k
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by • 0
0
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0
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1.3k
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Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
7.0 years ago mstagliamonte ▴ 10
0
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1
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1.6k
views
metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
7.0 years ago slizo001 • 0
2
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1
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1.6k
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Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 7.1 years ago by ★ 3.6k • written 7.1 years ago by ▴ 870
0
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1
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1.4k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
0
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1
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2.1k
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DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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0
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1.8k
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Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
7.7 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.8k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
7.8 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.8k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
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1
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2.3k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 8.1 years ago by ▴ 280 • written 8.1 years ago by ▴ 10
3
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2
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4.3k
views
DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
0
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6
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2.2k
views
Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
8.5 years ago lanhuong ▴ 20
0
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3
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2.2k
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Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 8.7 years ago by ★ 13k • written 8.7 years ago by • 0
1
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1
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4.4k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.7 years ago stats134711 • 0
0
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2
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1.9k
views
metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
9.0 years ago Brian Smith ▴ 120
8
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1
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4.4k
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 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 30
0
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5
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4.4k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by • 0
0
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8
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4.1k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 9.3 years ago by ★ 13k • written 12.0 years ago by 43k
0
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0
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1.7k
views
Job: 2 year bioinformatics postdoc in the microbiome and prostate cancer risk @ UEA, Norwich, UK
Cancer microbiome postdoc UK prostate cancer Job
9.3 years ago Daniel Brewer ▴ 100
4
votes
3
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2.6k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
0
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5
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2.0k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 10
2
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1
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2.2k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 10.3 years ago by 43k • written 10.3 years ago by • 0
1
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2
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2.4k
views
Normalization factors in metagenomeSeq
microbiome
10.7 years ago jovel_juan ▴ 30
2
votes
4
replies
2.9k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 3.0 years ago by • 0 • written 10.8 years ago by ▴ 30
1
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1
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3.7k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 10.9 years ago by ▴ 280 • written 10.9 years ago by ▴ 30
61 results • Page 1 of 2
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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