Showing : DESEq2 • reset
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how to save results meta data to file
DESeq2
written 3.8 years ago by ▴ 20
2
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17
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3.3k
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How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 3.7 years ago by • 0
2
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2
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2.8k
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Time series and interaction in DESeq2
DESeq2
3.7 years ago Francesco ▴ 10
0
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2
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2.4k
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DESeq2 Log2 fold change does not make sense given change in TPM
DESeq2 TPM Foldchange
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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2
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2.0k
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DESeq2 comparisons with multiple experimental variables?
DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
0
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1
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969
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DeSeq2 timecourse analysis
RNAseqRData DeSeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
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2
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1.3k
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Setting up read count data for DESeq2 to create a dds object
DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
1
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1
reply
983
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mgcv not loading on an update
m1_arm deseq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
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1
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794
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DESeq how to evaluate design fit
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 20
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4
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1.6k
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
3.7 years ago sushimoto • 0
0
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1
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982
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DEG for multiple comparisons
DESeq2
3.7 years ago rand.alkaissy • 0
0
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2
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1.3k
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Subsetting DESEQ2 VST Microbiome Data
DESeq2 16S VST
3.7 years ago vollkorrn • 0
0
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5
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2.7k
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DESeqDataSetFromMatrix Function Error
DESeq2 Bioconductor
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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3
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1.3k
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DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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2
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2.9k
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DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3.7 years ago by • 0 • written 9.3 years ago by ▴ 50
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1
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1.1k
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DESeq2 With Ratios from Nascent RNA-seq (Conversion Rate from slamdunk)
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 30
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5
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Error:The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as …
deseq2
updated 3.7 years ago by • 0 • written 5.1 years ago by • 0
2
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2
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901
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Salmon counts for a gene but it is not in my DESeq2 tables
DESeq2
3.7 years ago tomtom ▴ 10
15
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18
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5.1k
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Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
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1
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1.1k
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LRT test in DESeq2 decide on the level of comparisons
DESeq2 LRT Model
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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8
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3.0k
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lfcShrink MA plot comparison
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
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4
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Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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6
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1.7k
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ScRNA sequencing data _Seurat_Object_DESEQ2_Analayis_DGE
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
6
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2
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981
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The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 30
4
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1
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3.7k
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
2
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4
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5.5k
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Making contrasts for multiple treatment groups using DESeq2
DESeq2
updated 3.2 years ago by 43k • written 3.7 years ago by • 0
4
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4
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1.3k
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Covariates to be included in DE model
DESeq2 limma
updated 2.8 years ago by 43k • written 3.7 years ago by • 0
0
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3
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1.6k
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dealing with outliers (deseq2)
maxcooks outliers zero counts DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
2
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2
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1.2k
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Confounding DE results with DESeq2
isoforms DESeq2
3.7 years ago arfranco ▴ 130
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1
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977
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Including covariates from bulkRNAseq deconvolution to look for differentially expressed genes
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
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1
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1.0k
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Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
4
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.7 years ago treebig44 ▴ 40
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3
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1.9k
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Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
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4
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Unable to run "library(DESeq2)" successfully
DESeq2
written 4.8 years ago by • 0
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1
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1.1k
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DESeq2 TimeCourse with alpha and ihw and genes that change up to a certain timepoint
TimeCourse DESeq2 Manual
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 110
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1.3k
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 3.7 years ago by • 0 • written 3.7 years ago by ▴ 10
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4
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1.4k
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Using DESeq2 to analyze m6A read counts from Nanopore sequencing
DESeq2
3.7 years ago YC • 0
0
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4
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1.6k
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DESeq2 pseudotime series design?
DESeq2 design
3.7 years ago jordi.planells • 0
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847
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Some warnings when downloading "DESeq2"
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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Deseq2 normalization steps
deseq2 normalization
updated 3.7 years ago by 43k • written 6.5 years ago by • 0
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1.3k
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scale of mu in assays(dds)
DESeq2
3.7 years ago chase.mateusiak • 0
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DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
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5
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DESeq2 and high prefiltering cutoff
DESeq2 prefiltering
3.7 years ago Chris • 0
4
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7
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2.2k
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DESeq2: Subset Results from 2-Factor Design
DESeq2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 30
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5
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First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
3.8 years ago • updated 3.6 years ago 9906201a ▴ 20
1
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1
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985
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Result table pvalue and adjusted p value
DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 50
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2
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959
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Differential expression in fixed windows
DESeq2 RNASeq
3.8 years ago anatmela • 0
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2
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12k
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
DESeq2
3.8 years ago Hanan • 0
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1
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1.2k
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DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
4
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3
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1.9k
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Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
DESeq2 idep RNASeqData
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by ▴ 10
4,839 results • Page 23 of 97
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Replies
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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