Showing : DEseq2 • reset
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Extracting interaction contrast when using user supplied model.matrix
DESeq2
updated 2.8 years ago by 43k • written 2.9 years ago by • 0
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3
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1.4k
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DESeq2 Installation Issue
DESeq2
updated 2.9 years ago by 16k • written 2.9 years ago by • 0
2
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4
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1.4k
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Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 2.8 years ago by 43k • written 2.9 years ago by • 0
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1
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840
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Rnaseq analysis using a continuous time series
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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2
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1.7k
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installing DESeq2 on Macbook R Studio
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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1
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470
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More information on results columns
DESeq2
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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1
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878
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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Do the count values should be only integer to be able to use DESeq2?
DESeq2
2.9 years ago Sep • 0
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5
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1.6k
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Error running DESeq2 on longitudinal data: Error in checkFullRank(modelMatrix)
DESeq2 longitudinal
updated 2.9 years ago by ★ 1.4k • written 2.9 years ago by ▴ 40
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1.2k
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.9 years ago by ★ 1.6k • written 2.9 years ago by ▴ 10
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7
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1.7k
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DESeq2: Repetitive padj values?
DESeq2
updated 2.8 years ago by 43k • written 2.9 years ago by ▴ 30
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1
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1.0k
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Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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3
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1.4k
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how to iterate all comparisons in group with "coef =" ?
DESeq2
updated 2.8 years ago by 43k • written 2.9 years ago by ▴ 10
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1
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2.9k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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1.1k
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Help for RNA sequencing analysis with DESEQ2
DESeq2 star differentiallyexpressed
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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3
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1.5k
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Bulk RNA seq with deseq2, rnaseqGene, or edgeR
DESeq2 edgeR rnaseqGene
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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1
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737
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Combining VST counts for replicates
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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1
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1.6k
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How to set threshold of padj value in DeSeq2
DESeq2 padj default
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
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1
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765
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Differential RNA seq on TCGA set
DESeq2 RNASeqData
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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470
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rlog() transformation works only when using DESeqDataSet, not matrix
DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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2
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766
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Differential expression between samples of the same group
DESeq2
2.9 years ago Oded • 0
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1.5k
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Missing transcript
DESeq2 tximport salmon
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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3
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1.6k
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Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
2.9 years ago Alexandre • 0
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4
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2.5k
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Inverted Log2FC values after DEseq2 analysis
DESeq2 Log2FC RNASeqData
2.9 years ago Iwan • 0
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3
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1.3k
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Differential gene expression analysis with data matrix generated with RSEM
DESeq2 edgeR
2.9 years ago ubjw24 • 0
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1
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1.1k
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Using the standard deviation of DESeq rlog transformed counts to identify genes for hierarchical clustering
DESeq2
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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3
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9.2k
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Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
2.9 years ago Jayesh Kumar • 0
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3
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1.4k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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4
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1.4k
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suggest to report differential count estimate in DESeq2
DESeq2
2.9 years ago Yongqing • 0
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5
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2.7k
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Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 21 months ago by 43k • written 2.9 years ago by • 0
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6
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1.7k
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low counts from microRNA seq
DESeq2 microRNA HTSeq
2.9 years ago abhay.kanodia • 0
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2
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1.5k
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DESeq2: overlap differentially expressed genes with and without interaction term
DESeq2
2.9 years ago xuscha • 0
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3
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4.1k
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Error in SummarizedExperiment in DESeq2
DESeq2
2.9 years ago Cherif • 0
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3
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1.6k
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DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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1.4k
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DeSeq2 and GenomicRange installation possible conflict with bioconductor version 3.16?
DESeq2 version3.16 installation bioconductor GenomicRange
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
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2
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2.2k
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running DESeq2 from nanopore wf-alignment workflow
DESeq2 NanoporeRNASeq
updated 2.9 years ago by 43k • written 3.0 years ago by • 0
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2
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1.4k
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Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 3.0 years ago by • 0 • written 3.4 years ago by • 0
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2
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1.3k
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TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 3.0 years ago by • 0 • written 3.0 years ago by ▴ 90
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3
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2.3k
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Unusual MA and volcano plots?
DESeq2 RNASeq
written 3.0 years ago by ▴ 10
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675
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How does DESeq2 handle multiple conditions in one design.
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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1
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1.1k
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Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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1
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909
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Using DESeq2 for time-series analysis with two conditions
DESeq2 RNASeqData
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
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1
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1.2k
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Log2FC in LRT vs Wald in multifactorial design
DESeq2 LRT multifactorial up/down-reg log2FC
updated 3.0 years ago by 68k • written 3.0 years ago by ▴ 10
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2
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1.3k
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Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize statistics DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
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2
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1.3k
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How to filter for counts in different columns
DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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3
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1.5k
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question about removing both known and unknown confounders
DESeq2 RUVSeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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2
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857
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checkFullRank(modelMatrix) while neither factor can be predicted from each other.
DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
1
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13
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2.9k
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Deseq2 , result() taking too long > 3hrs
DESeq2
updated 2.8 years ago by • 0 • written 3.0 years ago by • 0
4
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8
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3.4k
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Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.5 years ago by 53k • written 3.0 years ago by ▴ 20
1
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3
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971
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DESeq2 on multiple sample groups
DESeq2
written 3.0 years ago by • 0
4,839 results • Page 16 of 97
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Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
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