Showing : DEseq2 • reset
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unreal negative log2fc values
DESeq2 des
updated 16 months ago by 68k • written 16 months ago by • 0
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1
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554
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 16 months ago by 43k • written 17 months ago by • 0
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8
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1.9k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 16 months ago by 53k • written 17 months ago by • 0
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2
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3.2k
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
17 months ago sropri • 0
0
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1
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564
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 17 months ago by 68k • written 17 months ago by • 0
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1
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764
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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5
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1.1k
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DESeq2 ML Query
DESeq2
updated 16 months ago by 43k • written 17 months ago by • 0
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3
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1.0k
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
17 months ago • updated 15 months ago David W. H. • 0
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1
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714
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
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3
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1.9k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
17 months ago Tanvi • 0
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1
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1.3k
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In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
2
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1
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676
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 10
2
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1
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813
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
1
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9
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3.2k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 17 months ago by 68k • written 17 months ago by ▴ 10
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3
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1.1k
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 17 months ago by 68k • written 17 months ago by ▴ 50
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6
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3.5k
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Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 17 months ago by ★ 5.0k • written 2.6 years ago by ▴ 20
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2
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925
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
17 months ago BioinfGuru ▴ 70
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2
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1.3k
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
17 months ago a_p • 0
0
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1
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724
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
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1
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641
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
1
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2
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2.8k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 17 months ago by ▴ 40 • written 6.1 years ago by • 0
0
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1
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520
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multiple condition issue running DESeq
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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3
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739
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Ploting of normalized counts after batch removal
DESeq2
updated 17 months ago by 53k • written 18 months ago by ▴ 10
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1
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490
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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669
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Best way to describe DEseq2 design
DESeq2
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
1
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2
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819
views
Deseq2
DESeq2 rnaseqGene
updated 18 months ago by ▴ 220 • written 18 months ago by • 0
1
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1
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571
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 18 months ago by 68k • written 18 months ago by ▴ 740
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6
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1.2k
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Counter-directional LFC shrinkage
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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1.2k
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
0
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3
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2.0k
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GSVA function
DESeq2 GSVA ssGSEA
updated 18 months ago by ★ 3.4k • written 18 months ago by • 0
0
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2
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970
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
18 months ago sukeshinik5 ▴ 20
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4
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2.2k
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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8
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1.3k
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
18 months ago boczniak767 ▴ 740
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3
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1.0k
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 18 months ago by 68k • written 18 months ago by ▴ 740
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6
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1.6k
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
18 months ago Ken C • 0
2
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4
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1.1k
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 18 months ago by 43k • written 18 months ago by • 0
4
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9
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1.4k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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3
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782
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by • 0
0
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1
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758
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 18 months ago by 43k • written 18 months ago by • 0
0
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9
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2.3k
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 17 months ago by ▴ 70 • written 18 months ago by • 0
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1.1k
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
18 months ago BioinfGuru ▴ 70
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1
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626
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
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1
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715
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
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7
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1.9k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 months ago sajadahmad41454 • 0
2
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1
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831
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Handling multiple differential expression comparisons
DESeq2
19 months ago • updated 17 months ago Zainab ▴ 20
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6
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1.1k
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 months ago by ★ 1.4k • written 19 months ago by ▴ 130
2
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6
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2.3k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 months ago by • 0 • written 19 months ago by • 0
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2
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524
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DESeq2 v1.35.0
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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2
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900
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Deseq2 and Normalization of RNA sequencing data
DESeq2
19 months ago kcarey • 0
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3
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1.4k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
4,839 results • Page 5 of 97
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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"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Comment: After running samtools, the featureCounts command crashed. by MarcHintz99 • 0
Thanks for shairng https://subread.sourceforge.net/
Comment: Senior Teaching Fellow (MSc Computational Biomedicine) by eja.ger.m • 0
Opportunities like this remind me how digital learning is evolving, much like modern mobile games. With programmes becoming fully online an…
Votes
Comment: upstream git branches of bioc-release
A: p.adjust BH generates duplicate values
Answer: gene Set with high AUC score but no cells assigned to cell type
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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