Showing : DESeq2 • reset
4
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9
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212
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 15 hours ago by ★ 4.1k • written 1 day ago by • 0
0
votes
3
replies
87
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 1 day ago by 42k • written 2 days ago by • 0
0
votes
1
reply
73
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 2 days ago by 42k • written 3 days ago by • 0
0
votes
8
replies
460
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 2 days ago by ▴ 30 • written 3 days ago by • 0
1
vote
2
replies
155
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
3 days ago • updated 9 hours ago BioinfGuru ▴ 30
0
votes
1
reply
152
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
0
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1
reply
95
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
2
votes
7
replies
352
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 days ago • updated 5 days ago sajadahmad41454 • 0
1
vote
1
reply
184
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Handling multiple differential expression comparisons
DESeq2
updated 11 days ago by 42k • written 13 days ago by ▴ 10
0
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6
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281
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 12 days ago by ★ 1.4k • written 14 days ago by ▴ 130
2
votes
3
replies
251
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 days ago by ★ 4.1k • written 13 days ago by • 0
0
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2
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157
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DESeq2 v1.35.0
DESeq2
updated 14 days ago by 42k • written 14 days ago by • 0
0
votes
2
replies
204
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Deseq2 and Normalization of RNA sequencing data
DESeq2
15 days ago • updated 14 days ago kcarey • 0
0
votes
3
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209
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
1
vote
3
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300
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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 8 days ago by ★ 4.1k • written 15 days ago by • 0
0
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3
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298
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
1
vote
1
reply
150
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
0
votes
2
replies
165
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
16 days ago • updated 13 days ago Aurora • 0
0
votes
1
reply
135
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
0
votes
1
reply
134
views
putting my own expression data in deseq2
DESeq2
updated 16 days ago by ★ 4.1k • written 16 days ago by • 0
3
votes
3
replies
264
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 17 days ago by ★ 4.1k • written 17 days ago by ▴ 10
0
votes
2
replies
225
views
PCA plot suggestions
DESeq2 PCAtools
updated 20 days ago by 42k • written 22 days ago by • 0
1
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3
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250
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 20 days ago by 42k • written 21 days ago by • 0
2
votes
9
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423
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 days ago by 65k • written 21 days ago by • 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 22 days ago by 42k • written 22 days ago by • 0
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 22 days ago by 42k • written 22 days ago by ▴ 20
1
vote
4
replies
353
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
22 days ago • updated 20 days ago winwater0928 • 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by 42k • written 23 days ago by ▴ 40
0
votes
8
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379
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 21 days ago by ★ 1.4k • written 23 days ago by • 0
3
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3
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249
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 23 days ago by 42k • written 24 days ago by • 0
0
votes
1
reply
153
views
rlog transformation
DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 28 days ago by 42k • written 28 days ago by • 0
1
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2
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737
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
29 days ago • updated 20 days ago Patadù ▴ 10
0
votes
1
reply
149
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covariate with negative and positive values
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
163
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 28 days ago by ★ 4.1k • written 29 days ago by • 0
0
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4
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261
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
29 days ago • updated 26 days ago lonn • 0
1
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2
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259
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 27 days ago Weiqian ▴ 10
0
votes
4
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291
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DEG with low counts
DESeq2
updated 27 days ago by 42k • written 4 weeks ago by • 0
1
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4
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518
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DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 15 days ago JKim • 0
0
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7
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444
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DESeq filtering specific to contrasts
DESeq2
updated 27 days ago by 42k • written 3 months ago by • 0
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 29 days ago by • 0 • written 11 months ago by • 0
0
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2
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1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 6 days ago by • 0 • written 15 months ago by ▴ 10
6
votes
19
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2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 16 days ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
5
replies
788
views
DESeq2 setting significant p-value
DESeq2
updated 27 days ago by 42k • written 5.0 years ago by ▴ 10
9
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12
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7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 28 days ago by • 0 • written 8.9 years ago by ▴ 30
45 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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