Showing : DeSeq2 • reset
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miRNA analysis with DESeq2
mirna DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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4
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1.2k
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different sample size from each individual
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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1
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810
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resultsNames(dds) is not similar to coldata(dds)?
DESeq2
3.6 years ago A.J. ▴ 20
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2
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1.8k
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How to get colData with GEOquery to prepare for DEseq2
GEOquery DEseq2
3.6 years ago Yugang • 0
1
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1
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850
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DESeq2 Multiple Pairwise Comparisons with Odd Set-up
MultipleComparison DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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2
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How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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5
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4.7k
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Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE DESeq2
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
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3
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3.3k
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installation of package ‘DESeq2’ had non-zero exit status
DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by ▴ 10
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1.8k
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trouble installing DESeq2
install packages R DESeq2
updated 3.6 years ago by 4.2k • written 3.6 years ago by • 0
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5
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13k
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is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by ▴ 10
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3
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Cannot install DESeq2 to R 4.2 version
DESeq2
updated 3.6 years ago by 4.2k • written 3.6 years ago by • 0
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1
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1.6k
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BaseMean and Log2FC values seem weird...
DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
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2
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941
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Volcano plots
DESeq2
written 3.6 years ago by • 0
1
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1
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961
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ChIRP-seq peaks and GSEA
DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
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1
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2.7k
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DESeq2- how to remove NA values
DESeq2
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
2
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3
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1.9k
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
3.6 years ago Maka • 0
1
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2
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1.5k
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Technical replicates of different library from same sample
DESeq2
3.6 years ago • updated 3.5 years ago myfam128 • 0
5
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14
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7.4k
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Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.6 years ago by ★ 5.0k • written 7.4 years ago by ▴ 60
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8
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3.6k
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Error in SummarizedExperiment
DESeq2
3.6 years ago Talpham • 0
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1
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3.9k
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DESeq2 installation Error (ERROR: dependency ‘locfit’ is not available for package ‘DESeq2’)
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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5
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3.4k
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DESeq2::plotPCA plotting error
RStudio PCA DESeq2
written 3.6 years ago by • 0
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583
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Deseq2 high outlier number
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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8
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6.1k
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deseq2 normalized counts as an input to deseq2
DESeq2
updated 2.7 years ago by 43k • written 3.6 years ago by • 0
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6
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6.9k
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BaseMean threshold
basemean DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.6 years ago by • 0
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3
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897
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Student
samples sampleNumbers DESeq2
written 3.6 years ago by • 0
10
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6
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16k
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DESEq2 VST error
deseq2 variancestabilizingtransformation
updated 3.3 years ago by • 0 • written 8.4 years ago by ▴ 70
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4
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1.5k
views
Extremely different results for both EdgeR and DESeq2 analysis
edgeR DESeq2
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
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3
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1.4k
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Why are padj results different for BetaPrior = TRUE vs lfcShrink()?
IHW lfcShrink DESeq2
3.6 years ago Ali Barry ▴ 40
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5
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2.1k
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Potential outlier/high variance
deseq DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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2
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2.5k
views
Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE
DESeq2
3.6 years ago ng.akingbesote • 0
16
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12
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4.0k
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VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
3.6 years ago Joan Miró ▴ 80
2
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1
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2.8k
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Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
1
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2
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3.0k
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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.6 years ago Ismail • 0
1
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7
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12k
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Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no pa…
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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5
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3.3k
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
3.6 years ago • updated 3.5 years ago priyanka.m • 0
1
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2
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1.1k
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how to change the FDR threshold in DESrq2?
DESeq2
3.6 years ago devi • 0
10
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11
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4.0k
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Counts from recount3 for DESeq2 analysis
recount3 DESeq2
updated 3.3 years ago by ★ 1.1k • written 3.6 years ago by ▴ 10
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3
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1.8k
views
lfcShrink contrast
lfcshrink R DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
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1
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1.3k
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DESeq2 with small sample size
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
3
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6
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2.6k
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Paired sample design in DESeq2
DESeq2
updated 3.6 years ago by ▴ 10 • written 4.0 years ago by • 0
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1
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881
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batch effects for a single sample?
DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by ▴ 10
2
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1
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1.4k
views
DESeq2
DESeq2
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
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2
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4.1k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 2.3 years ago by • 0 • written 3.6 years ago by • 0
0
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2
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1.6k
views
Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 3.6 years ago by 43k • written 3.7 years ago by ▴ 40
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1
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1.1k
views
Getting erros from dds
DifferentialExpression DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
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3
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1.2k
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DESeq2 relevel question and resultsNames
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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4
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1.2k
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DESeq2 Volcano - Quick Question
DESeq2
3.7 years ago axe880 • 0
0
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7
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2.1k
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DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.6 years ago by 43k • written 3.7 years ago by • 0
0
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1
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1.4k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
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2
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1.9k
views
filterbyexprs before DESeq2
DESeq2
3.7 years ago luca.s ▴ 50
4,840 results • Page 22 of 97
Recent ...
Replies
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…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
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
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
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