Showing : Metagenomics • reset
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 12 days ago by • 0 • written 10 months ago by • 0
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2
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510
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Job: Postdoc and Bioinformatician position in metagenomic data analysis available
Metagenomics curatedMetagenomicData bugsigdbr
written 4 months ago by ★ 1.1k
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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
8 months ago Mohamed ▴ 30
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4
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744
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How do I design my DESEQ experiment?
DESeq2 Metagenomics
14 months ago • updated 13 months ago Michael • 0
0
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0
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537
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ALDEx2 Error Message: "dim(X) must have a positive length" when using aldex.clr() with denom="iqlr"
Metagenomics IQLR ALDEx2
16 months ago cwarden45 • 0
1
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0
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611
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Shotgun metagenomics data analysis
Metagenomics abundance
18 months ago YASIR ▴ 10
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2
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1.2k
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How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics DESeq2
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
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1
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897
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
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1
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817
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
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1
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2.1k
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Import MetaPhlAn3 to Phyloseq
Metaphlan3 Metagenomics phyloseq
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by • 0
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951
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Pattern Search in MicrobiomeAnalyst
metagenomeSeq Metagenomics microbiome microbiomeExplorer
2.8 years ago GlycineMax • 0
0
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1
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766
views
FDR Correction
dada2 Metagenomics DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
3
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3
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1.2k
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Using DESeq2 to identify changing transcriptional activity in a metagenome
Metagenomics DESeq2 Metatranscriptomics
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
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0
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984
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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.1 years ago jol.espinoz ▴ 40
15
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4
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32k
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Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.7 years ago by ▴ 190 • written 3.7 years ago by ▴ 10
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1
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1.1k
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Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
1
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1
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1.2k
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WGCNA threshold without prior knowledge of scale-free propery
wgcna weighted correlation network analysis correlation matrix scale-free topology metagenomics
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by • 0
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1.3k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
6.2 years ago jol.espinoz ▴ 40
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1.3k
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Job: Bioinformatics Specialist at the University of Illinois
job bioinformatics microbiome metagenomics epigenomics Job
6.2 years ago Jenny Drnevich ★ 2.0k
1
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1
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1.7k
views
Should I normalize communities separately with metagenomeseq?
metagenomeseq microbiome gut microbiome metagenomics shotgun metagenomics
updated 6.4 years ago by ▴ 280 • written 6.4 years ago by ▴ 10
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11
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2.2k
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DESeq2 on 16S copy number corrected genes
deseq2 metagenomics
updated 6.6 years ago by 41k • written 6.7 years ago by ▴ 10
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3
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1.9k
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Error bars on DESeq2 visuals
deseq2 metagenomics phyloseq ggplot2
6.7 years ago lauren.czaplicki • 0
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1.3k
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Phylogenetic tree from marker genes
ape phyloseq dist metagenomics
7.0 years ago David ▴ 860
3
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5
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2.4k
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DESeq2 to clustered metagenomic data
deseq2 metagenomics
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
2
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3
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6.2k
views
DESEq2 error when performing exploratory analysis with no replicates
software error deseq2 metagenomics
updated 7.4 years ago by 41k • written 7.4 years ago by • 0
0
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5
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1.8k
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MetagenomSeq, perform anova or kruskall wallis with three groups ?
metagenomeseq anova metagenomics
8.0 years ago David ▴ 860
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2
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1.9k
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Advice on normalization with metagenomics data
metagenome normalization metagenomics
8.0 years ago David ▴ 860
4
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4
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3.3k
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edgeR and gene filtering
edger metagenomics gene abundance gene filtering
8.5 years ago jtremblay514 • 0
0
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1
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1.3k
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Influence of average genome size on DESeq2 results
deseq2 normalization metagenomics
updated 8.5 years ago by 41k • written 8.5 years ago by • 0
8
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Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.8 years ago Martin Morgan 25k
2
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8
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3.3k
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edgeR for metagenomic data
edger metagenomics
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ▴ 70
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5
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2.9k
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baySeq issues and questions
bayseq metagenomics
9.5 years ago • updated 9.2 years ago lordbleys • 0
0
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2
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4.4k
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Pathway enrichment in bacteria metagenomes
pathways metagenomics
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
5
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5
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2.0k
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Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
9.6 years ago patrick.schordert ▴ 30
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1
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1.5k
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mouseData in heatmap of metagenomeSeq package
Metagenomics metagenomeSeq Metagenomics metagenomeSeq
updated 10.1 years ago by ▴ 280 • written 10.1 years ago by ★ 13k
35 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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