Showing : Deseq2 • reset
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119
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by 66k • written 2 days ago by ▴ 720
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6
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572
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 1 day ago Ken C • 0
2
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4
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199
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
4
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9
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301
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 7 days ago by • 0
0
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3
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145
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 days ago by 42k • written 7 days ago by • 0
0
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1
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111
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 7 days ago by 42k • written 8 days ago by • 0
0
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8
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541
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 7 days ago by ▴ 30 • written 8 days ago by • 0
1
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2
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265
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
8 days ago • updated 5 days ago BioinfGuru ▴ 30
0
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1
reply
189
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 12 days ago by ★ 4.1k • written 12 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 13 days ago by ★ 4.1k • written 13 days ago by • 0
2
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7
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435
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
14 days ago • updated 10 days ago sajadahmad41454 • 0
1
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1
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197
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Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
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6
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309
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
2
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3
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265
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
0
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2
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176
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DESeq2 v1.35.0
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
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2
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219
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Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
0
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3
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231
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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 20 days ago by • 0
1
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3
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313
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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 14 days ago by ★ 4.1k • written 20 days ago by • 0
0
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3
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308
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
1
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1
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161
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
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2
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174
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
22 days ago • updated 19 days ago Aurora • 0
0
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1
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142
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 22 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 22 days ago by • 0
3
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3
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276
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 23 days ago by ★ 4.1k • written 23 days ago by ▴ 10
0
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2
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230
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PCA plot suggestions
DESeq2 PCAtools
updated 25 days ago by 42k • written 27 days ago by • 0
1
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3
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259
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 26 days ago by • 0
2
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9
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432
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 26 days ago by 66k • written 26 days ago by • 0
0
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1
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168
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 27 days ago by 42k • written 27 days ago by • 0
1
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3
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242
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Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by 42k • written 28 days ago by ▴ 20
1
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4
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363
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 days ago winwater0928 • 0
3
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1
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330
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 28 days ago by 42k • written 28 days ago by ▴ 40
0
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8
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404
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 27 days ago by ★ 1.4k • written 28 days ago by • 0
3
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3
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256
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
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1
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160
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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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132
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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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762
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago Patadù ▴ 10
0
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1
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151
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covariate with negative and positive values
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
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171
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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
0
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4
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272
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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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236
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
1
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2
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268
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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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295
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DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
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153
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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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217
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Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago hemantcnaik • 0
0
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1
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155
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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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202
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DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
0
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2
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250
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 6 weeks ago by 42k • written 6 weeks ago by ▴ 30
0
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1
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196
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 6 weeks ago by 42k • written 6 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 6 weeks ago by 42k • written 6 weeks ago by • 0
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
Recent ...
Replies
Comment: recount3 problem downloading data from source sra by PABLO ANTONIO • 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working by websterdelacruz2087055 • 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Comment: slingshot: error with plot3d.SlingshotDataSet by Happiness • 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Votes
Answer: recount3 problem downloading data from source sra
Answer: recount3 problem downloading data from source sra
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
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