Showing : microbiome • reset
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 16 months ago by 68k • written 16 months ago by • 0
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3
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2.0k
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 19 months ago by • 0 • written 2.7 years ago by • 0
1
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1
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756
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 22 months ago by ▴ 40 • written 22 months ago by ★ 1.6k
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2
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1.5k
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DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
2.3 years ago anton.kratz ▴ 60
2
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1
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2.5k
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Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq microbiome Software
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
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0
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963
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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
2.5 years ago Mohamed ▴ 30
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2
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3.2k
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
3.0 years ago Elif • 0
1
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0
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1.0k
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News: Virtual talk “Model Misspecification in Microbiome Studies” by Amy D Willis
MicrobiomeData Microbiome
3.2 years ago Levi Waldron ★ 1.1k
1
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3
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9.4k
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 3.4 years ago by ▴ 40 • written 5.3 years ago by • 0
0
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1
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1.3k
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How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
0
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3
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2.9k
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I cannot install "microbiome"
GenomeInfoDbData microbiome phyloseq
updated 3.5 years ago by 700 • written 3.5 years ago by • 0
2
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1
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3.1k
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Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 10
0
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1
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1.4k
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DESeq2 differences in Wald and LRT in multi-factorial design
microbiome LRT DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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1
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994
views
pairwise within sample
DESeq2 microbiome
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
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1
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1.6k
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Editing Plots Generated Using MicrobiomeAnalyst
MicrobiomeData microbiome offtopic
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
0
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1
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1.5k
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Adding insect abundance data to SparCC Analysis
sparcc Microbiome microbiomeExplorer MicrobiomeData
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
0
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0
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1.6k
views
Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
4.7 years ago GlycineMax • 0
0
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0
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1.6k
views
News: Early career researchers: nominate to present your work at BVCN virtual conference on microbiome research
microbiome news Conference
5.0 years ago Matthew Ritchie ▴ 1000
0
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2
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1.7k
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Question: export edgeR normalised OTU table
microbiome edgeR
5.0 years ago Pozdrawiam • 0
0
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2
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2.7k
views
Differential Abundance Analysis wih DESeq2 and metabolites as continuous predictor variables
deseq2 microbiome R
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
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1
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1.8k
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MetagenomeSeq: analysing paired samples
metagenomeseq paired samples microbiome
updated 5.9 years ago by • 0 • written 9.2 years ago by • 0
0
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2
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1.4k
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DESeq2: seeking advice regarding before/after mutliple treatements + extra factor
deseq2 16s microbiome
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 10
0
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0
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1.4k
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Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
6.1 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
6.3 years ago supindab ▴ 10
0
votes
2
replies
1.9k
views
DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
6.6 years ago zhigang.li • 0
0
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2
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2.1k
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DESeq2 Interaction Term Interpretation for Microbiome Data
deseq2 microbiome
updated 6.7 years ago by ★ 1.4k • written 6.7 years ago by • 0
0
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0
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1.4k
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Aldex2 feature request - controlling for additional variables
ALDEx2 ALDEx microbiome 16s
7.2 years ago mstagliamonte ▴ 10
0
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1
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1.7k
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metagenomeSeq error question: error on creation of newMRexperiment
metagenomeseq error metagenomeseq microbiome
7.2 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 7.3 years ago by ★ 3.6k • written 7.3 years ago by ▴ 870
0
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1
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1.5k
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Question about multi-factor Deseq analysis
DESeq deseq2 microbiome gut microbiome
updated 7.3 years ago by 43k • written 7.3 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 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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0
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1.9k
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Job: EXTENDED: Bioinformatics Specialist at the University of Illinois
microbiome epigenomics bioinformatics analyst NGS Job
7.9 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.9k
views
Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
8.0 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.9k
views
Getting OTUID rather than Taxonomy from Results function in DESeq2
deseq2 R microbiome phyloseq qiime
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
1
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1
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2.4k
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Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by ▴ 10
3
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2
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4.4k
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DESeq2 iterative size factor normalization did not converge
deseq2 microbiome phyloseq
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
0
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6
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2.3k
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Why DESeq2 gives large logfold for group with all zero count?
microbiome 16s deseq2 differential gene expression
8.7 years ago lanhuong ▴ 20
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3
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2.4k
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Where to find open access microbiome data for case-control comparative study?
microbiome data analysis data request
updated 8.8 years ago by ★ 13k • written 8.8 years ago by • 0
1
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1
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4.5k
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Normalization/Transformation Before Microbiome Alpha Diversity Analysis
microbiome normalization variancestabilizingtransformation phyloseq
8.9 years ago stats134711 • 0
0
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2
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2.0k
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metagenomeSeq: cumNormStat normalization default
metagenomeseq microbiome
9.2 years ago Brian Smith ▴ 120
8
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1
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4.6k
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 9.4 years ago by ★ 13k • written 9.4 years ago by ▴ 30
0
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5
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4.7k
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DESeq2 16s microbiome size factors
deseq2 metagenomeseq rnaseq 16s microbiome
updated 9.5 years ago by ▴ 280 • written 9.5 years ago by • 0
0
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8
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4.3k
views
Variance stabilizing transformation seems not working on NGS (bacterial 16srRNA based) data
Microbiome DESeq2 Microbiome DESeq2
updated 9.5 years ago by ★ 13k • written 12.2 years ago by 43k
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0
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1.7k
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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
9.5 years ago Daniel Brewer ▴ 100
4
votes
3
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2.8k
views
Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
0
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5
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2.1k
views
deseq2 analysis, accounting for pen effect
deseq2 microbiome
updated 10.3 years ago by ★ 13k • written 10.3 years ago by ▴ 10
2
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1
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2.3k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 10.4 years ago by 43k • written 10.4 years ago by • 0
1
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2
replies
2.5k
views
Normalization factors in metagenomeSeq
microbiome
10.9 years ago • updated 10.8 years ago jovel_juan ▴ 30
2
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4
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3.0k
views
normFactors when aggregating in metagenomeSeq
metagenomeSeq microbiome
updated 3.2 years ago by • 0 • written 11.0 years ago by ▴ 30
1
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1
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3.8k
views
Low quantile estimate using CSS normalization in metagenomeSeq
metagenomeSeq microbiome
updated 11.1 years ago by ▴ 280 • written 11.1 years ago by ▴ 30
61 results • Page 1 of 2
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Answer: Unable to create venndiagram using VennDiagram 1.5.1 package by kesha • 0
<a href=https://vavadacasinox.com/>vavadacasinox.com</a>
Comment: How to convert .raw data for use in xcms by a2a2asawhaa • 0
try converting your files to the older mzXML format, which remains highly stable for XCMS. While waiting for large datasets to process, you…
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
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Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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