Showing : desEQ2 • reset
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
updated 4 hours ago by ★ 4.2k • written 4 hours ago by • 0
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2
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70
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 15 hours ago by 42k • written 16 hours ago by • 0
1
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8
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144
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
2 days ago • updated 1 day ago boczniak767 ▴ 720
1
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3
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145
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 3 days ago by 66k • written 4 days ago by ▴ 720
2
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4
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218
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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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604
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
7 days ago • updated 3 days ago Ken C • 0
1
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2
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274
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
10 days ago • updated 7 days ago BioinfGuru ▴ 30
4
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9
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323
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 8 days ago by ★ 4.2k • written 9 days ago by • 0
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3
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159
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 9 days ago by 42k • written 9 days ago by • 0
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8
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569
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 9 days ago by ▴ 30 • written 10 days ago by • 0
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1
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121
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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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449
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
16 days ago • updated 13 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 14 days ago by • 0 • written 16 months ago by ▴ 10
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1
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197
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 14 days ago by ★ 4.2k • written 14 days ago by • 0
0
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1
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121
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 15 days ago by ★ 4.2k • written 15 days ago by • 0
1
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3
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321
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 16 days ago by ★ 4.2k • written 22 days ago by • 0
1
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1
reply
199
views
Handling multiple differential expression comparisons
DESeq2
updated 19 days ago by 42k • written 20 days ago by ▴ 10
2
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3
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270
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 19 days ago by ★ 4.2k • written 20 days ago by • 0
0
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6
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314
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 20 days ago by ★ 1.4k • written 21 days ago by ▴ 130
0
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2
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179
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
24 days ago • updated 21 days ago Aurora • 0
0
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2
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220
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Deseq2 and Normalization of RNA sequencing data
DESeq2
22 days ago • updated 21 days ago kcarey • 0
0
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2
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183
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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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241
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 22 days ago by ★ 4.2k • written 22 days ago by • 0
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3
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310
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
1
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4
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538
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DEseq2 coefficient
DESeq2 coefficient
3 months ago • updated 22 days ago JKim • 0
6
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19
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2.6k
views
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 4.7 years ago by ▴ 10
1
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1
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162
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 24 days ago by 42k • written 24 days ago by • 0
0
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1
reply
144
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 24 days ago by 42k • written 24 days ago by • 0
0
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1
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143
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putting my own expression data in deseq2
DESeq2
updated 24 days ago by ★ 4.2k • written 24 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 25 days ago by ★ 4.2k • written 25 days ago by ▴ 10
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2
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233
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PCA plot suggestions
DESeq2 PCAtools
updated 27 days ago by 42k • written 29 days ago by • 0
1
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2
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775
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 28 days ago Patadù ▴ 10
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3
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261
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 28 days ago by 42k • written 28 days ago by • 0
1
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4
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367
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 weeks ago • updated 28 days ago winwater0928 • 0
2
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9
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449
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 28 days ago by 66k • written 29 days ago by • 0
0
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8
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412
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 29 days ago by ★ 1.4k • written 4 weeks ago by • 0
0
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1
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170
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 29 days ago by 42k • written 29 days ago by • 0
1
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3
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247
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Different Shrunk Log2FC according with reference
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
3
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1
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339
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 40
3
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3
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264
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
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4
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276
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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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275
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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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804
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DESeq2 setting significant p-value
DESeq2
updated 5 weeks ago by 42k • written 5.1 years ago by ▴ 10
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4
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298
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DEG with low counts
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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1
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162
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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
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134
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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
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154
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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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172
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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
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error when running topGO with KS statistic and elim agorithm by James W. MacDonald 66k
You'll probably have to figure this out yourself. That error is coming from a non-exported function called `.sigGroups.elim`, which iterate…
Answer: Cluster columns in Pheatmap by James W. MacDonald 66k
This support site is meant for helping people with Bioconductor packages, and `pheatmap` isn't one of them, so you should be posting on bio…
Comment: Cluster columns in Pheatmap by elefth.pavlos ▴ 40
Hi, You mean to take the average expression of each group per gene and plot only 2 columns with averages?
Answer: Normalisation using clinical traits in RNA seq using DESeq2 by ATpoint ★ 4.2k
See the vignette, it's a FAQ: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-st…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Please could you comment on this @rory
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Awards • All
Popular Question to kevin.rue ▴ 350
Popular Question to Wei Shi ★ 3.6k
Popular Question to Gordon Smyth 50k
Popular Question to jovel_juan ▴ 30
Scholar to ATpoint ★ 4.2k
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