Showing : DESEQ2 • reset
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resultsNames(dds) is not similar to coldata(dds)?
DESeq2
3.5 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
3.5 years ago Yugang • 0
1
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1
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843
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DESeq2 Multiple Pairwise Comparisons with Odd Set-up
MultipleComparison DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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2
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1.7k
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How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
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5
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4.6k
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Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE DESeq2
updated 3.5 years ago by ▴ 780 • written 3.5 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 3.5 years ago by ★ 5.0k • written 3.5 years ago by ▴ 10
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1
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1.7k
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trouble installing DESeq2
install packages R DESeq2
updated 3.5 years ago by 4.2k • written 3.5 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 3.5 years ago by ★ 1.4k • written 3.5 years ago by ▴ 10
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3
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3.2k
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Cannot install DESeq2 to R 4.2 version
DESeq2
updated 3.5 years ago by 4.2k • written 3.5 years ago by • 0
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1.6k
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BaseMean and Log2FC values seem weird...
DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
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2
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931
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Volcano plots
DESeq2
written 3.5 years ago by • 0
1
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1
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954
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ChIRP-seq peaks and GSEA
DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 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 3.5 years ago by ★ 4.0k • written 3.5 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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1.4k
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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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3.5k
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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
4
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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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1
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577
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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 2.6 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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894
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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 8.3 years ago by ▴ 70
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4
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1.5k
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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
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Error in DESeq(dds) : is(object, "DESeqDataSet") is not TRUE
DESeq2
3.6 years ago ng.akingbesote • 0
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12
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3.9k
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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
views
Deseq2 for 16s Data
Microbiome 16s Deseq2 16srRNA
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
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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 3.5 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
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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 • updated 3.5 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 3.2 years ago by ★ 1.1k • written 3.6 years ago by ▴ 10
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3
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1.7k
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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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1.2k
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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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863
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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
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1
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1.3k
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 2.2 years ago by • 0 • written 3.6 years ago by • 0
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2
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1.6k
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Condition shown as 'Untreated vs. Treated' in output of results() in DESeq2
RNASeqData DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 40
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1
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1.1k
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Getting erros from dds
DifferentialExpression DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 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 3.6 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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DESeq2 Volcano - Quick Question
DESeq2
3.6 years ago axe880 • 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 3.6 years ago by • 0
0
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1
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1.3k
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
3
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2
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1.9k
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filterbyexprs before DESeq2
DESeq2
3.6 years ago luca.s ▴ 50
0
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1
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905
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How to add new column name to empty header in a list elements
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
2
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4
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1.4k
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how to save results meta data to file
DESeq2
written 3.8 years ago by ▴ 20
4,838 results • Page 22 of 97
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Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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