Showing : desEQ2 • reset
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GSVA function
DESeq2 GSVA ssGSEA
updated 1 hour ago by ★ 3.3k • written 2 hours ago by • 0
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36
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
updated 7 hours ago by ★ 4.2k • written 7 hours ago by • 0
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2
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74
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 18 hours ago by 42k • written 20 hours ago by • 0
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8
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146
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
2 days ago • updated 1 day ago boczniak767 ▴ 720
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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 5 days ago by ▴ 720
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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 4 days ago Ken C • 0
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4
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219
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 4 days ago by 42k • written 7 days ago by • 0
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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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122
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 10 days ago by 42k • written 11 days ago by • 0
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8
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570
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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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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 8 days ago BioinfGuru ▴ 30
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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
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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
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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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199
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Handling multiple differential expression comparisons
DESeq2
updated 19 days ago by 42k • written 21 days ago by ▴ 10
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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
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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 21 days ago by • 0
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2
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183
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DESeq2 v1.35.0
DESeq2
updated 22 days ago by 42k • written 22 days ago by • 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
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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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321
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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 16 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
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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
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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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1
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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
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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 28 days ago by 42k • written 29 days ago by • 0
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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
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9
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450
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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
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171
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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 4 weeks ago by • 0
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3
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248
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Different Shrunk Log2FC according with reference
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
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4
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369
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
4 weeks ago • updated 28 days ago winwater0928 • 0
3
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1
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339
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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
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8
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417
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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
3
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3
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267
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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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162
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rlog transformation
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 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
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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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154
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covariate with negative and positive values
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 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
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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
0
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3
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237
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
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2
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276
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How to retrieve detailed regression results from deseq2
DESeq2
6 weeks ago • updated 4 weeks ago Weiqian ▴ 10
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4
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299
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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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156
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Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
1
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2
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218
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Design Matrix within group comparison more than two groups
DESeq2
6 weeks ago • updated 5 weeks ago hemantcnaik • 0
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1
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156
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Bioinformatics student
Des DESeq2
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
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1
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203
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DESeq2 gives an error and R crashes
DESeq2
6 weeks ago Shefali • 0
50 results • Page 1 of 1
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Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
What version of zlib are you running? I can compile with 1.2.7
Comment: SingleR Label.Ont by Anna • 0
It makes me happy that I have finally found a trusted and safe online casino in Australia. I read a lot of different additional information…
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…
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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
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