Showing : DEseq2 • reset
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
47 minutes ago • updated 41 minutes ago i.sudbery ▴ 30
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
3 hours ago Aaliya • 0
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3
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122
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 5 hours ago by 41k • written 1 day ago by • 0
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82
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rlog transformation
DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
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1
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79
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 days ago by 41k • written 5 days ago by • 0
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
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103
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covariate with negative and positive values
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
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1
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108
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 5 days ago by ★ 4.0k • written 6 days ago by • 0
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4
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181
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 days ago • updated 3 days ago lonn • 0
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3
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167
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 7 days ago by 41k • written 8 days ago by ▴ 20
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215
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How to retrieve detailed regression results from deseq2
DESeq2
12 days ago • updated 3 days ago Weiqian ▴ 10
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4
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225
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DEG with low counts
DESeq2
updated 4 days ago by 41k • written 8 days ago by • 0
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1
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108
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Deseq2 Rlog transformation
DESeq2
updated 8 days ago by ★ 4.0k • written 9 days ago by • 0
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2
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163
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Design Matrix within group comparison more than two groups
DESeq2
11 days ago • updated 10 days ago hemantcnaik • 0
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115
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Bioinformatics student
Des DESeq2
updated 11 days ago by • 0 • written 11 days ago by • 0
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152
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DESeq2 gives an error and R crashes
DESeq2
12 days ago • updated 11 days ago Shefali • 0
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2
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191
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 13 days ago by 41k • written 18 days ago by ▴ 30
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1
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135
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 13 days ago by 41k • written 14 days ago by • 0
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2
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218
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Regressing out batch effects
DESeq2
updated 13 days ago by 41k • written 19 days ago by • 0
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2
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141
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 18 days ago by 65k • written 18 days ago by • 0
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1
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152
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DESeq2 - Missing values in count matrix
DESeq2
updated 19 days ago by 65k • written 19 days ago by • 0
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6
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400
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 19 days ago by 41k • written 20 days ago by • 0
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135
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
21 days ago • updated 20 days ago Layal • 0
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2
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149
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
21 days ago • updated 20 days ago michelafrancesconi8 • 0
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4
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228
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 21 days ago by 41k • written 21 days ago by • 0
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140
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 25 days ago by 41k • written 25 days ago by • 0
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3
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320
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PCA of different bacterial species
DESeq2
updated 27 days ago by 41k • written 27 days ago by ▴ 10
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1
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157
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collapseReplicates dimension error
DESeq2 Dese
updated 28 days ago by 41k • written 4 weeks ago by • 0
3
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2
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196
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
29 days ago Anita ▴ 10
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211
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 27 days ago Chanderkant Chaudhary • 0
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406
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 28 days ago fr8712ca-s • 0
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7
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383
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DESeq filtering specific to contrasts
DESeq2
updated 4 days ago by 41k • written 9 weeks ago by • 0
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4
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563
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 7 days ago by 41k • written 6 months ago by • 0
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 22 days ago by ★ 13k • written 9 months ago by ▴ 10
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5
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 6 days ago by • 0 • written 10 months ago by • 0
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16
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2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 hours ago by 41k • written 4.6 years ago by ▴ 10
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5
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692
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DESeq2 setting significant p-value
DESeq2
updated 4 days ago by 41k • written 5.0 years ago by ▴ 10
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 days ago by • 0 • written 8.8 years ago by ▴ 30
38 results • Page 1 of 1
Recent ...
Replies
Answer: List of Deprecated Packages for Bioc3.19 by shepherl 3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
It is indeed better. Anyway, did you notice this part in the output from `str(ortologos_filtrados)`: `$Gene.ID : int 115709372 115716460 …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
I'm new here, but its better now?
Votes
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
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