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 16 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
views
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
168
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
3 days ago • updated 10 hours ago BioinfGuru ▴ 30
0
votes
1
reply
152
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
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
353
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 days ago • updated 5 days ago sajadahmad41454 • 0
1
vote
1
reply
184
views
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
votes
2
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157
views
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
replies
300
views
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
replies
298
views
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
views
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 18 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
vote
3
replies
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
replies
423
views
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
replies
379
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 22 days ago by ★ 1.4k • written 23 days ago by • 0
3
votes
3
replies
249
views
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
vote
2
replies
737
views
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
views
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
votes
4
replies
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
0
votes
3
replies
226
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by ▴ 20
1
vote
2
replies
259
views
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
views
DEG with low counts
DESeq2
updated 27 days ago by 42k • written 4 weeks ago by • 0
0
votes
1
reply
144
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
1
vote
2
replies
211
views
Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago hemantcnaik • 0
0
votes
1
reply
149
views
Bioinformatics student
Des DESeq2
updated 4 weeks ago by • 0 • written 4 weeks ago by • 0
0
votes
1
reply
193
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
0
votes
2
replies
243
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 30
0
votes
1
reply
185
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
2
replies
264
views
Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
182
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
vote
1
reply
187
views
DESeq2 - Missing values in count matrix
DESeq2
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
1
vote
6
replies
455
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
1
vote
1
reply
171
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
6 weeks ago Layal • 0
50 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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