Showing : microbiome • reset
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153
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 22 days ago by ▴ 40 • written 22 days ago by ★ 1.5k
0
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2
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751
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 3 days ago by • 0 • written 11 months ago by • 0
0
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2
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522
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DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
6 months ago anton.kratz ▴ 60
2
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1
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1.1k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 8 months ago by ★ 4.1k • written 8 months ago by ▴ 10
0
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0
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384
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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
9 months ago Mohamed ▴ 30
0
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2
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1.4k
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
15 months ago Elif • 0
1
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0
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519
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
17 months ago Levi Waldron ★ 1.1k
1
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3
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7.0k
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 19 months ago by ▴ 30 • written 3.6 years ago by • 0
0
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1
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709
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 20 months ago by 65k • written 20 months ago by • 0
0
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3
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1.7k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 21 months ago by 700 • written 21 months ago by • 0
2
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1
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1.7k
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Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 2.1 years ago by 42k • written 2.1 years ago by ▴ 10
0
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1
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823
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
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1
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588
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pairwise within sample
DESeq2 microbiome
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
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1
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920
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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1
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890
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Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
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0
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982
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.9 years ago GlycineMax • 0
0
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0
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1.0k
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News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
3.3 years ago Matthew Ritchie ▴ 1000
0
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2
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1.2k
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Question: export edgeR normalised OTU table
microbiome edgeR
3.3 years ago Pozdrawiam • 0
0
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2
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1.6k
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Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 3.7 years ago by 42k • written 3.7 years ago by • 0
0
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1
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1.3k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 4.1 years ago by • 0 • written 7.4 years ago by • 0
0
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2
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864
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 4.3 years ago by 42k • written 4.3 years ago by ▴ 10
0
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0
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950
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
4.4 years ago lhuang7 ▴ 50
1
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0
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892
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Job: Bioinformatician: NEW YORK CITY - Institute for Data Science and Genomic Technology, Mount Sinai School of Medicine
job bioinformatician systems biology microbiome genomics Job
4.6 years ago supindab ▴ 10
0
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2
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1.3k
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.9 years ago zhigang.li • 0
0
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2
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1.5k
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by • 0
0
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0
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918
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Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
5.4 years ago mstagliamonte ▴ 10
0
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1
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1.1k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
5.4 years ago slizo001 • 0
2
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1
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1.1k
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Rsubread for microbiome data analysis: genome >4GB
alignment rsubread microbiome
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 850
0
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1
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1.0k
views
Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
0
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1
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1.6k
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DeSeq2 for comparison of experimental factors on microbial composition
deseq2 microbiome fungi fungal microbiome
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
0
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0
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1.3k
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Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
6.1 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.3k
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.3 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.4k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 6.5 years ago by 42k • written 6.5 years ago by • 0
1
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1
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1.8k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
3
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2
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3.3k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
0
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6
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1.6k
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Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
6.9 years ago lanhuong ▴ 20
0
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3
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1.6k
views
Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 7.1 years ago by ★ 13k • written 7.1 years ago by • 0
1
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1
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3.5k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
7.1 years ago stats134711 • 0
0
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2
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1.5k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
7.5 years ago Brian Smith ▴ 120
6
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1
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3.3k
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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 7.6 years ago by ★ 13k • written 7.6 years ago by ▴ 20
0
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5
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3.6k
views
DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
0
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8
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3.3k
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Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 7.8 years ago by ★ 13k • written 10.5 years ago by 42k
0
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0
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1.3k
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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
7.8 years ago Daniel Brewer ▴ 100
4
votes
3
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2.0k
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Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 7.9 years ago by 42k • written 7.9 years ago by • 0
0
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5
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1.6k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 10
2
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1
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1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.7 years ago by 42k • written 8.7 years ago by • 0
1
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2
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1.9k
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Normalization factors in metagenomeSeq
microbiome
9.1 years ago jovel_juan ▴ 30
2
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4
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2.3k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 17 months ago by • 0 • written 9.3 years ago by ▴ 30
1
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1
reply
3.1k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
1
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1
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1.6k
views
Problem reproducing metagenomeSeq tutorial example
metagenome microbiome metagenomeseq
updated 9.3 years ago by ▴ 280 • written 9.3 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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