Showing : DESeq2 • reset
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
1 day ago • updated 21 hours ago boczniak767 ▴ 720
1
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3
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137
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 2 days ago by 66k • written 4 days ago by ▴ 720
2
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4
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217
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 3 days ago by 42k • written 6 days ago by • 0
0
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6
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595
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
6 days ago • updated 3 days ago Ken C • 0
1
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2
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271
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
9 days ago • updated 7 days ago BioinfGuru ▴ 30
4
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9
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313
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 7 days ago by ★ 4.2k • written 8 days ago by • 0
0
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3
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154
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 8 days ago by 42k • written 9 days ago by • 0
0
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8
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557
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 8 days ago by ▴ 30 • written 10 days ago by • 0
0
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1
reply
117
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 9 days ago by 42k • written 10 days ago by • 0
2
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7
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443
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
15 days ago • updated 12 days ago sajadahmad41454 • 0
0
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2
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1.5k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 13 days ago by • 0 • written 16 months ago by ▴ 10
0
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1
reply
192
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 13 days ago by ★ 4.2k • written 13 days ago by • 0
0
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1
reply
120
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 14 days ago by ★ 4.2k • written 14 days ago by • 0
1
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3
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320
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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 15 days ago by ★ 4.2k • written 21 days ago by • 0
1
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1
reply
199
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Handling multiple differential expression comparisons
DESeq2
updated 18 days ago by 42k • written 20 days ago by ▴ 10
2
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3
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267
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 18 days ago by ★ 4.2k • written 20 days ago by • 0
0
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6
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312
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 19 days ago by ★ 1.4k • written 20 days ago by ▴ 130
0
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2
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176
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
23 days ago • updated 20 days ago Aurora • 0
0
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2
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219
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Deseq2 and Normalization of RNA sequencing data
DESeq2
21 days ago • updated 20 days ago kcarey • 0
0
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2
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182
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DESeq2 v1.35.0
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
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3
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238
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 21 days ago by ★ 4.2k • written 21 days ago by • 0
0
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3
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309
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 21 days ago by 42k • written 22 days ago by • 0
1
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4
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537
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DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 22 days ago JKim • 0
6
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19
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2.6k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 23 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
1
reply
162
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 23 days ago by 42k • written 23 days ago by • 0
0
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1
reply
143
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 23 days ago by 42k • written 23 days ago by • 0
0
votes
1
reply
143
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putting my own expression data in deseq2
DESeq2
updated 23 days ago by ★ 4.2k • written 23 days ago by • 0
3
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3
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279
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 24 days ago by ★ 4.2k • written 24 days ago by ▴ 10
0
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2
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232
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PCA plot suggestions
DESeq2 PCAtools
updated 27 days ago by 42k • written 28 days ago by • 0
1
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2
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767
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 27 days ago Patadù ▴ 10
1
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3
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261
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 27 days ago by 42k • written 27 days ago by • 0
1
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4
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365
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
29 days ago • updated 27 days ago winwater0928 • 0
2
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9
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444
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 27 days ago by 66k • written 28 days ago by • 0
0
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8
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407
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 28 days ago by ★ 1.4k • written 4 weeks ago by • 0
0
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1
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170
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 28 days ago by 42k • written 29 days ago by • 0
1
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3
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243
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Different Shrunk Log2FC according with reference
DESeq2
updated 29 days ago by 42k • written 29 days ago by ▴ 20
3
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1
reply
335
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by ▴ 40
3
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3
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262
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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4
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273
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
5 weeks ago • updated 4 weeks ago lonn • 0
1
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2
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273
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How to retrieve detailed regression results from deseq2
DESeq2
6 weeks ago • updated 4 weeks ago Weiqian ▴ 10
0
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7
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461
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DESeq filtering specific to contrasts
DESeq2
updated 4 weeks ago by 42k • written 3 months ago by • 0
2
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5
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803
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DESeq2 setting significant p-value
DESeq2
updated 4 weeks ago by 42k • written 5.0 years ago by ▴ 10
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4
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296
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DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
reply
160
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rlog transformation
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
reply
133
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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
0
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1
reply
151
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covariate with negative and positive values
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
9
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12
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7.9k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 30
0
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1
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171
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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
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 5 weeks ago by • 0 • written 11 months ago by • 0
0
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4
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638
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 5 weeks ago by 42k • written 7 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res by jovel_juan ▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by ATpoint ★ 4.2k
SAF files must not have a header.
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by xuz • 0
Could you try the latest version (1.40.1) to see how it works, I am not able to replicate the error message on my computer here.
Comment: Not able to install any Bioconductor 3.18 package [unable to access index] by merv ▴ 120
Thanks! I can confirm it is working now - had been broken since sometime yesterday.
Comment: Errors in chromosome annotation-biomaRt by landenshanie ▴ 40
Thank you, I ran your exact code and it correct for Xist, however Ddx3y is still wrongly annotated to chr13 and, like your results, Dusp1 i…
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
Error when converting Seurat to SingleCellExperiment
Comment: unable to access bioconductor packages - qvalue installation failed...
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