Showing : Deseq2 • reset
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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
16 months ago sropri • 0
0
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1
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554
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 16 months ago by 68k • written 16 months ago by • 0
1
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1
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745
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
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5
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1.1k
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DESeq2 ML Query
DESeq2
updated 15 months ago by 43k • written 16 months ago by • 0
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3
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992
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
16 months ago • updated 15 months ago David W. H. • 0
0
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1
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689
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 16 months ago by 68k • written 16 months ago by • 0
1
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3
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1.9k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
16 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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651
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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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799
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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
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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 16 months ago by 68k • written 17 months ago by ▴ 10
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3
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1.0k
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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
3
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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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911
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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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1.2k
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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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671
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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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630
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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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2.7k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 17 months ago by ▴ 40 • written 6.0 years ago by • 0
0
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1
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512
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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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728
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Ploting of normalized counts after batch removal
DESeq2
updated 17 months ago by 53k • written 17 months ago by ▴ 10
1
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1
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483
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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2
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655
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Best way to describe DEseq2 design
DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
1
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2
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805
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Deseq2
DESeq2 rnaseqGene
updated 17 months ago by ▴ 220 • written 17 months ago by • 0
1
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1
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561
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 17 months ago by 68k • written 17 months ago by ▴ 740
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6
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1.1k
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Counter-directional LFC shrinkage
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
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3
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1.9k
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GSVA function
DESeq2 GSVA ssGSEA
updated 17 months ago by ★ 3.4k • written 17 months ago by • 0
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2
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952
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
17 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 17 months ago by ★ 5.0k • written 17 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
17 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 17 months ago by 68k • written 17 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 • updated 17 months ago Ken C • 0
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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 17 months ago by 43k • written 17 months ago by • 0
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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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768
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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
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1
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742
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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
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9
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2.2k
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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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2
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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
0
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1
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614
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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1
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702
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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
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 months ago sajadahmad41454 • 0
2
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1
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819
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Handling multiple differential expression comparisons
DESeq2
18 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 18 months ago by ▴ 130
2
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6
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2.2k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 months ago by • 0 • written 18 months ago by • 0
0
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2
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514
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DESeq2 v1.35.0
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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884
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Deseq2 and Normalization of RNA sequencing data
DESeq2
18 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 18 months ago by ★ 5.0k • written 18 months ago by • 0
1
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3
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3.3k
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
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3
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694
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
3
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1
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866
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 18 months ago by 43k • written 18 months ago by ▴ 10
4,836 results • Page 5 of 97
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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