Showing : DESEq2 • reset
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 15 hours ago by 66k • written 1 day ago by ▴ 720
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6
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554
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 18 hours ago Ken C • 0
2
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4
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179
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 17 hours ago by 42k • written 3 days ago by • 0
4
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9
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282
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 4 days ago by ★ 4.1k • written 6 days ago by • 0
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3
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134
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 5 days ago by 42k • written 6 days ago by • 0
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1
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105
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 6 days ago by 42k • written 7 days ago by • 0
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8
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528
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 6 days ago by ▴ 30 • written 7 days ago by • 0
1
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2
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256
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
7 days ago • updated 4 days ago BioinfGuru ▴ 30
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1
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186
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
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1
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116
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
2
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7
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423
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 9 days ago sajadahmad41454 • 0
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1
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195
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Handling multiple differential expression comparisons
DESeq2
updated 15 days ago by 42k • written 17 days ago by ▴ 10
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6
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306
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 18 days ago by ▴ 130
2
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3
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262
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
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2
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175
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DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
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217
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Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
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3
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230
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
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3
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306
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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 13 days ago by ★ 4.1k • written 19 days ago by • 0
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3
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305
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
1
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1
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160
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
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2
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172
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 18 days ago Aurora • 0
0
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1
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140
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
0
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1
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141
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putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
3
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3
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275
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 22 days ago by ▴ 10
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2
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229
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PCA plot suggestions
DESeq2 PCAtools
updated 24 days ago by 42k • written 26 days ago by • 0
1
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3
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257
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 24 days ago by 42k • written 25 days ago by • 0
2
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9
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429
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 25 days ago by 66k • written 25 days ago by • 0
0
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1
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167
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 26 days ago by 42k • written 26 days ago by • 0
1
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3
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240
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Different Shrunk Log2FC according with reference
DESeq2
updated 26 days ago by 42k • written 27 days ago by ▴ 20
1
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4
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362
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago winwater0928 • 0
3
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1
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329
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 40
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8
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395
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 26 days ago by ★ 1.4k • written 27 days ago by • 0
3
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3
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254
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 27 days ago by 42k • written 28 days ago by • 0
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1
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158
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rlog transformation
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
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130
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
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2
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756
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 24 days ago Patadù ▴ 10
0
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1
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149
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covariate with negative and positive values
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
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169
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
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4
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271
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago lonn • 0
0
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3
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233
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by ▴ 20
1
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266
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago Weiqian ▴ 10
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4
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293
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DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
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1
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150
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Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
1
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2
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215
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Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago hemantcnaik • 0
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1
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153
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Bioinformatics student
Des DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
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1
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201
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DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
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2
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248
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
0
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1
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193
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
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2
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267
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Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
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2
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184
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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