Showing : DEseq2 • reset
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 18 hours ago by 66k • written 22 hours ago by • 0
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3
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152
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 1 day ago by 66k • written 1 day ago by ▴ 50
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6
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1.7k
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Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 1 day ago by ★ 4.2k • written 14 months ago by ▴ 20
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2
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93
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
3 days ago • updated 2 days ago BioinfGuru ▴ 30
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80
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
5 days ago hx ▴ 10
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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
5 days ago prabath_meemaduma • 0
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
7 days ago • updated 5 days ago a_p • 0
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96
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 5 days ago by ★ 1.4k • written 6 days ago by • 0
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108
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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 6 days ago by 66k • written 6 days ago by • 0
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1.9k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 7 days ago by ▴ 40 • written 4.6 years ago by • 0
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122
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multiple condition issue running DESeq
DESeq2
updated 9 days ago by 42k • written 9 days ago by • 0
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208
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Ploting of normalized counts after batch removal
DESeq2
updated 9 days ago by 51k • written 11 days ago by ▴ 10
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129
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 12 days ago by 42k • written 13 days ago by • 0
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167
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Best way to describe DEseq2 design
DESeq2
updated 13 days ago by ★ 1.4k • written 13 days ago by • 0
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178
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Deseq2
DESeq2 rnaseqGene
updated 13 days ago by ▴ 210 • written 13 days ago by • 0
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 14 days ago by 66k • written 15 days ago by ▴ 730
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6
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315
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Counter-directional LFC shrinkage
DESeq2
updated 13 days ago by 42k • written 15 days ago by • 0
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204
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 16 days ago by ★ 4.0k • written 18 days ago by • 0
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3
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239
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GSVA function
DESeq2 GSVA ssGSEA
updated 17 days ago by ★ 3.3k • written 19 days ago by • 0
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2
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186
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
20 days ago • updated 17 days ago sukeshinik5 • 0
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4
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369
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 18 days ago by ★ 4.2k • written 20 days ago by • 0
1
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8
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280
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
21 days ago boczniak767 ▴ 730
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230
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 23 days ago by 66k • written 24 days ago by ▴ 730
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6
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680
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
27 days ago • updated 23 days ago Ken C • 0
2
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292
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 23 days ago by 42k • written 26 days ago by • 0
4
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9
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367
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 27 days ago by ★ 4.2k • written 29 days ago by • 0
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3
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192
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 29 days ago by 42k • written 29 days ago by • 0
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1
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149
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 29 days ago by 42k • written 4 weeks ago by • 0
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9
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783
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 10 days ago by ▴ 30 • written 4 weeks ago by • 0
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2
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308
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
4 weeks ago • updated 27 days ago BioinfGuru ▴ 30
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1
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227
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by • 0
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1
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154
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
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7
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544
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 weeks ago • updated 4 weeks ago sajadahmad41454 • 0
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2
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270
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Handling multiple differential expression comparisons
DESeq2
5 weeks ago • updated 16 hours ago Zainab ▴ 10
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6
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358
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by ▴ 130
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3
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323
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
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2
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208
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DESeq2 v1.35.0
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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2
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252
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Deseq2 and Normalization of RNA sequencing data
DESeq2
6 weeks ago • updated 5 weeks ago kcarey • 0
0
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3
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289
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
1
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3
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386
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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 5 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
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3
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334
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
1
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1
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197
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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208
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
6 weeks ago • updated 5 weeks ago Aurora • 0
0
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1
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156
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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1
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158
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putting my own expression data in deseq2
DESeq2
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
3
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3
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303
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by ▴ 10
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2
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257
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PCA plot suggestions
DESeq2 PCAtools
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
1
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3
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283
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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9
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484
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
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1
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196
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Behaviour of featureCounts when quantifying multi-mapping reads by Rachael • 0
Thank you so much for your help!
Comment: EnhancedVolcano results in an empty plot by Patadù ▴ 10
Hi James, I do not know if it might be of interest for you, but in the end I could plot the Volcano plot. I did have to use the `lfcShrink(…
Answer: Behaviour of featureCounts when quantifying multi-mapping reads by Yang Liao ▴ 420
Both `v1.5.0` and `v1.6.4` versions are very old. I suggest upgrading to `v2.0.6` (the latest version). There was a change regarding the `…
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr by Ozan • 0
Sounds good. Thanks again!
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr by James W. MacDonald 66k
Ah, ok. Doesn't really matter though. Try using `UniProt.ws`.
Votes
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
A: How to do a confounding variable adjustment without using the treatment informat
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
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