Showing : DeSeq2 • reset
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 15 months ago by 68k • written 15 months ago by • 0
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714
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 15 months ago by ★ 4.9k • written 15 months ago by • 0
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5
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1.1k
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DESeq2 ML Query
DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
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3
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938
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
15 months ago • updated 14 months ago David W. H. • 0
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647
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
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3
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1.8k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
15 months ago Tanvi • 0
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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 15 months ago by 43k • written 16 months ago by • 0
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615
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 15 months ago by 43k • written 16 months ago by ▴ 10
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1
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762
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by ▴ 70
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9
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3.1k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 15 months ago by 68k • written 15 months ago by ▴ 10
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3
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937
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 16 months ago by 68k • written 16 months ago by ▴ 50
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6
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3.4k
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Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 16 months ago by ★ 4.9k • written 2.5 years ago by ▴ 20
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2
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846
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
16 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
16 months ago a_p • 0
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585
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
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608
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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 16 months ago by 68k • written 16 months ago by • 0
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2
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2.6k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 16 months ago by ▴ 40 • written 5.9 years ago by • 0
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496
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multiple condition issue running DESeq
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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3
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705
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Ploting of normalized counts after batch removal
DESeq2
updated 16 months ago by 53k • written 16 months ago by ▴ 10
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1
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454
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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636
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Best way to describe DEseq2 design
DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
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2
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771
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Deseq2
DESeq2 rnaseqGene
updated 16 months ago by ▴ 220 • written 16 months ago by • 0
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542
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 16 months ago by 68k • written 16 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 16 months ago by 43k • written 16 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 16 months ago by ★ 4.1k • written 16 months ago by • 0
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3
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1.9k
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GSVA function
DESeq2 GSVA ssGSEA
updated 16 months ago by ★ 3.4k • written 16 months ago by • 0
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2
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918
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
16 months ago sukeshinik5 ▴ 20
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4
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2.1k
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
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8
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1.2k
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
16 months ago boczniak767 ▴ 740
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3
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978
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 16 months ago by 68k • written 16 months ago by ▴ 740
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1.5k
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
16 months ago Ken C • 0
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4
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1.0k
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 16 months ago by 43k • written 16 months ago by • 0
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9
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1.3k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
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3
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740
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 16 months ago by 43k • written 16 months ago by • 0
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704
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 16 months ago by 43k • written 16 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 16 months ago by ▴ 70 • written 16 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
16 months ago BioinfGuru ▴ 70
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587
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
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1
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676
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 17 months ago by ★ 4.9k • written 17 months ago by • 0
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7
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1.8k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
17 months ago sajadahmad41454 • 0
2
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1
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794
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Handling multiple differential expression comparisons
DESeq2
17 months ago • updated 15 months ago Zainab ▴ 20
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1.1k
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 months ago by ★ 1.4k • written 17 months ago by ▴ 130
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6
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2.1k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 7 months ago by • 0 • written 17 months ago by • 0
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2
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497
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DESeq2 v1.35.0
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
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2
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860
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Deseq2 and Normalization of RNA sequencing data
DESeq2
17 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 17 months ago by ★ 4.9k • written 17 months ago by • 0
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3
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3.1k
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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 17 months ago by ★ 4.9k • written 17 months ago by • 0
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3
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675
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
3
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1
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836
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 months ago by 43k • written 17 months ago by ▴ 10
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2
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949
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
17 months ago Aurora • 0
4,835 results • Page 5 of 97
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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