Showing : deseq2 • reset
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
3 days ago • updated 8 hours ago BioinfGuru ▴ 30
4
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9
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212
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 15 hours ago by ★ 4.1k • written 1 day ago by • 0
0
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3
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87
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 1 day ago by 42k • written 2 days ago by • 0
0
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8
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460
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 2 days ago by ▴ 30 • written 3 days ago by • 0
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1
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73
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 2 days ago by 42k • written 3 days ago by • 0
2
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7
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352
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 days ago • updated 5 days ago sajadahmad41454 • 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 6 days ago by • 0 • written 15 months ago by ▴ 10
0
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1
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152
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
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1
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95
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
1
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3
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300
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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 8 days ago by ★ 4.1k • written 15 days ago by • 0
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1
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184
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Handling multiple differential expression comparisons
DESeq2
updated 11 days ago by 42k • written 13 days ago by ▴ 10
2
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3
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251
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 days ago by ★ 4.1k • written 13 days ago by • 0
0
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6
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281
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 12 days ago by ★ 1.4k • written 14 days ago by ▴ 130
0
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2
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164
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
16 days ago • updated 13 days ago Aurora • 0
0
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2
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204
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Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago kcarey • 0
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2
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157
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DESeq2 v1.35.0
DESeq2
updated 14 days ago by 42k • written 14 days ago by • 0
0
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3
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208
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
0
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3
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298
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
1
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4
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518
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DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 15 days ago JKim • 0
6
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19
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2.5k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by • 0 • written 4.6 years ago by ▴ 10
1
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1
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150
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
0
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1
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135
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
0
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1
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134
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putting my own expression data in deseq2
DESeq2
updated 16 days ago by ★ 4.1k • written 16 days ago by • 0
3
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3
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264
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 17 days ago by ★ 4.1k • written 17 days ago by ▴ 10
0
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2
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225
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PCA plot suggestions
DESeq2 PCAtools
updated 20 days ago by 42k • written 22 days ago by • 0
1
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2
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737
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
29 days ago • updated 20 days ago Patadù ▴ 10
1
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3
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250
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 20 days ago by 42k • written 21 days ago by • 0
1
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4
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353
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
22 days ago • updated 20 days ago winwater0928 • 0
2
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9
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423
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 days ago by 65k • written 21 days ago by • 0
0
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8
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379
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 21 days ago by ★ 1.4k • written 23 days ago by • 0
0
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1
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165
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 22 days ago by 42k • written 22 days ago by • 0
1
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3
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234
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Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by 42k • written 22 days ago by ▴ 20
3
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1
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328
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by 42k • written 23 days ago by ▴ 40
3
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3
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249
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 23 days ago by 42k • written 24 days ago by • 0
0
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4
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261
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
29 days ago • updated 26 days ago lonn • 0
1
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2
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259
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 27 days ago Weiqian ▴ 10
0
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7
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444
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DESeq filtering specific to contrasts
DESeq2
updated 27 days ago by 42k • written 3 months ago by • 0
2
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5
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788
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DESeq2 setting significant p-value
DESeq2
updated 27 days ago by 42k • written 5.0 years ago by ▴ 10
0
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4
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291
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DEG with low counts
DESeq2
updated 27 days ago by 42k • written 4 weeks ago by • 0
0
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1
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153
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rlog transformation
DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
0
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1
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124
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 28 days ago by 42k • written 28 days ago by • 0
0
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1
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149
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covariate with negative and positive values
DESeq2
updated 28 days ago by 42k • written 4 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 28 days ago by • 0 • written 8.9 years ago by ▴ 30
0
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1
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163
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 28 days ago by ★ 4.1k • written 29 days 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 29 days ago by • 0 • written 11 months ago by • 0
0
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4
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628
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 4 weeks ago by 42k • written 6 months ago by • 0
0
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3
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226
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
0
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1
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144
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
1
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2
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211
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Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago hemantcnaik • 0
0
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1
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149
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Bioinformatics student
Des DESeq2
updated 4 weeks ago by • 0 • written 4 weeks ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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