Showing : DESeq2 • reset
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
1 hour ago Sara • 0
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1
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51
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GSVA function
DESeq2 GSVA ssGSEA
updated 1 day ago by ★ 3.3k • written 1 day ago by • 0
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1
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55
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
updated 1 hour ago by ★ 4.2k • written 1 day ago by • 0
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4
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149
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 1 hour ago by ★ 4.2k • written 2 days ago by • 0
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8
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163
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
3 days ago boczniak767 ▴ 720
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155
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 5 days ago by 66k • written 6 days ago by ▴ 720
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6
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616
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
9 days ago • updated 5 days ago Ken C • 0
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4
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228
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 5 days ago by 42k • written 8 days ago by • 0
4
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9
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330
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 9 days ago by ★ 4.2k • written 11 days ago by • 0
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3
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163
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 10 days ago by 42k • written 11 days ago by • 0
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1
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124
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 11 days ago by 42k • written 12 days ago by • 0
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8
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573
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 11 days ago by ▴ 30 • written 12 days ago by • 0
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2
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277
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
12 days ago • updated 9 days ago BioinfGuru ▴ 30
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1
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201
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 16 days ago by ★ 4.2k • written 16 days ago by • 0
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1
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123
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 17 days ago by ★ 4.2k • written 17 days ago by • 0
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7
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 days ago • updated 14 days ago sajadahmad41454 • 0
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1
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199
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Handling multiple differential expression comparisons
DESeq2
updated 20 days ago by 42k • written 22 days ago by ▴ 10
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6
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320
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 22 days ago by ★ 1.4k • written 23 days ago by ▴ 130
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3
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276
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 21 days ago by ★ 4.2k • written 22 days ago by • 0
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2
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187
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DESeq2 v1.35.0
DESeq2
updated 23 days ago by 42k • written 23 days ago by • 0
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2
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222
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Deseq2 and Normalization of RNA sequencing data
DESeq2
24 days ago • updated 23 days ago kcarey • 0
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3
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245
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 23 days ago by ★ 4.2k • written 24 days ago by • 0
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3
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325
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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 days ago by ★ 4.2k • written 24 days ago by • 0
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3
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310
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
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1
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164
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 25 days ago by 42k • written 25 days ago by • 0
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2
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181
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
26 days ago • updated 23 days ago Aurora • 0
0
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1
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144
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 25 days ago by 42k • written 26 days ago by • 0
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1
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143
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putting my own expression data in deseq2
DESeq2
updated 25 days ago by ★ 4.2k • written 26 days ago by • 0
3
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3
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281
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 27 days ago by ★ 4.2k • written 27 days ago by ▴ 10
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2
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239
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PCA plot suggestions
DESeq2 PCAtools
updated 29 days ago by 42k • written 4 weeks ago by • 0
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3
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262
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 29 days ago by 42k • written 4 weeks ago by • 0
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9
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460
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
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176
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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3
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249
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Different Shrunk Log2FC according with reference
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
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4
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374
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 weeks ago winwater0928 • 0
3
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1
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342
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 40
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8
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423
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 4 weeks ago by ★ 1.4k • written 4 weeks ago by • 0
3
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3
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268
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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1
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162
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rlog transformation
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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1
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137
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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779
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 29 days ago Patadù ▴ 10
0
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1
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154
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covariate with negative and positive values
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
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172
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
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4
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279
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
5 weeks ago lonn • 0
0
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3
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237
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
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2
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277
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How to retrieve detailed regression results from deseq2
DESeq2
6 weeks ago • updated 5 weeks ago Weiqian ▴ 10
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4
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303
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DEG with low counts
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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1
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158
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Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
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2
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218
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Design Matrix within group comparison more than two groups
DESeq2
6 weeks ago hemantcnaik • 0
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1
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156
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Bioinformatics student
Des DESeq2
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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