Showing : deseq2 • reset
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 16 months ago by 68k • written 16 months ago by • 0
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1
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729
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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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959
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
16 months ago • updated 14 months ago David W. H. • 0
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1
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667
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 16 months ago by 68k • written 16 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
16 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 16 months ago by 43k • written 16 months ago by • 0
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1
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627
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 16 months ago by 43k • written 16 months ago by ▴ 10
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1
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781
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 16 months ago by 68k • written 16 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 16 months ago by 68k • written 16 months ago by ▴ 10
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3
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952
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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 ★ 5.0k • written 2.6 years ago by ▴ 20
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2
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869
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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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597
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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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623
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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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2.7k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 16 months ago by ▴ 40 • written 6.0 years ago by • 0
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1
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506
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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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719
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Ploting of normalized counts after batch removal
DESeq2
updated 16 months ago by 53k • written 16 months ago by ▴ 10
1
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1
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472
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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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651
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Best way to describe DEseq2 design
DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
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2
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792
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Deseq2
DESeq2 rnaseqGene
updated 17 months ago by ▴ 220 • written 17 months ago by • 0
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1
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557
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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
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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
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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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932
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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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2.1k
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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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1.2k
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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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992
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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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1.5k
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
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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1.3k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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3
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754
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 17 months ago by 43k • written 17 months ago by • 0
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730
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 17 months ago by 43k • written 17 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 17 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
17 months ago BioinfGuru ▴ 70
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1
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600
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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1
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691
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
2
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7
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1.9k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
17 months ago sajadahmad41454 • 0
2
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1
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807
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Handling multiple differential expression comparisons
DESeq2
17 months ago • updated 16 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 17 months ago by ★ 1.4k • written 17 months ago by ▴ 130
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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 7 months ago by • 0 • written 17 months ago by • 0
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2
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507
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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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872
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Deseq2 and Normalization of RNA sequencing data
DESeq2
18 months ago • updated 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 ★ 5.0k • written 18 months ago by • 0
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3
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3.2k
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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 ★ 5.0k • written 18 months ago by • 0
0
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3
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690
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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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849
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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
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2
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964
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
18 months ago • updated 17 months ago Aurora • 0
4,835 results • Page 5 of 97
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Answer: Issue with Soft-Thresholding in WGCNA by misty.chickadee.vckc • 0
Hi Maria, your detailed explanation is super helpful! The NA power estimate in WGCNA can be tricky. I've sometimes seen that when the data …
Comment: Interpretation of output of AffyRNAdeg and hist commands by debasainalsa • 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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