Showing : DESeq2 • reset
4
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9
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209
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 14 hours ago by ★ 4.1k • written 1 day ago by • 0
0
votes
3
replies
86
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
457
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
142
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
3 days ago • updated 8 hours ago BioinfGuru ▴ 30
0
votes
1
reply
151
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
352
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
votes
6
replies
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
replies
156
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
replies
206
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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
299
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
votes
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
164
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
133
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 21 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 21 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
242
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
263
views
Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
181
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!!
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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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