Showing : DEseq2 • reset
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 14 hours ago by 66k • written 1 day ago by ▴ 720
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5
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123
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Counter-directional LFC shrinkage
DESeq2
1 day ago • updated 14 hours ago ennui • 0
0
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2
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121
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 2 days ago by ★ 4.0k • written 3 days ago by • 0
0
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3
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145
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GSVA function
DESeq2 GSVA ssGSEA
updated 2 days ago by ★ 3.3k • written 5 days ago by • 0
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2
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120
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
5 days ago • updated 2 days ago sukeshinik5 • 0
0
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4
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254
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 3 days ago by ★ 4.2k • written 6 days ago by • 0
1
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8
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202
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
7 days ago boczniak767 ▴ 720
1
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3
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184
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 9 days ago by 66k • written 10 days ago by ▴ 720
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6
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634
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
12 days ago • updated 9 days ago Ken C • 0
2
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4
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257
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 9 days ago by 42k • written 12 days ago by • 0
4
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9
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344
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 13 days ago by ★ 4.2k • written 14 days ago by • 0
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3
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174
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 14 days ago by 42k • written 15 days ago by • 0
0
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1
reply
132
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 15 days ago by 42k • written 16 days ago by • 0
0
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8
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589
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 15 days ago by ▴ 30 • written 16 days ago by • 0
1
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2
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288
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
16 days ago • updated 13 days ago BioinfGuru ▴ 30
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1
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205
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 19 days ago by ★ 4.2k • written 19 days ago by • 0
0
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1
reply
127
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 20 days ago by ★ 4.2k • written 20 days ago by • 0
2
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7
replies
487
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
21 days ago • updated 18 days ago sajadahmad41454 • 0
1
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1
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205
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Handling multiple differential expression comparisons
DESeq2
updated 24 days ago by 42k • written 26 days ago by ▴ 10
0
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6
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326
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 26 days ago by ★ 1.4k • written 27 days ago by ▴ 130
2
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3
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285
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 24 days ago by ★ 4.2k • written 26 days ago by • 0
0
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2
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189
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DESeq2 v1.35.0
DESeq2
updated 27 days ago by 42k • written 27 days ago by • 0
0
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2
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227
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Deseq2 and Normalization of RNA sequencing data
DESeq2
28 days ago • updated 27 days ago kcarey • 0
0
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3
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254
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 27 days ago by ★ 4.2k • written 28 days ago by • 0
1
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3
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344
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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 21 days ago by ★ 4.2k • written 28 days ago by • 0
0
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3
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316
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
1
vote
1
reply
168
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 29 days ago by 42k • written 29 days ago by • 0
0
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2
replies
186
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
29 days ago • updated 26 days ago Aurora • 0
0
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1
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147
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
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1
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145
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putting my own expression data in deseq2
DESeq2
updated 29 days ago by ★ 4.2k • written 29 days ago by • 0
3
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3
replies
287
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by ▴ 10
0
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2
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245
views
PCA plot suggestions
DESeq2 PCAtools
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
1
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3
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269
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
2
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9
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465
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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
0
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1
reply
181
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
1
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3
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253
views
Different Shrunk Log2FC according with reference
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
1
vote
4
replies
377
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
5 weeks ago • updated 4 weeks ago winwater0928 • 0
3
votes
1
reply
350
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 40
0
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8
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431
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
3
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3
replies
276
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
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166
views
rlog transformation
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
143
views
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
1
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2
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789
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
6 weeks ago • updated 4 weeks ago Patadù ▴ 10
0
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1
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156
views
covariate with negative and positive values
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
1
reply
177
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
0
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4
replies
287
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 weeks ago • updated 5 weeks ago lonn • 0
0
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3
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240
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 20
1
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2
replies
280
views
How to retrieve detailed regression results from deseq2
DESeq2
7 weeks ago • updated 5 weeks ago Weiqian ▴ 10
0
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4
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309
views
DEG with low counts
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
1
reply
160
views
Deseq2 Rlog transformation
DESeq2
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
50 results • Page 1 of 1
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Comment: How to run allelic imbalance in apeglm by parayod376 • 0
Which I care about. [Papa's games][1] thank you for sharing the information. [1]: https://papasgamesfree.github.io
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
FYI, I emailed Benilton and he says he's working on a fix, so stay tuned!
Answer: Error in render R qmd document (could not find function "process") by James W. MacDonald 66k
If you have functions in another R document, you have to `source` that document to load the functions into your workspace. Just like you wo…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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