Showing : DESEQ2 • reset
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PCA plot suggestions
DESeq2 PCAtools
updated 1 hour ago by 41k • written 1 day ago by • 0
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
9 days ago • updated 2 hours ago ussarizona ▴ 10
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 3 hours ago by 41k • written 20 hours ago by • 0
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180
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
2 days ago • updated 10 hours ago winwater0928 • 0
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9
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 21 hours ago by 65k • written 1 day ago by • 0
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 1 day ago by ★ 1.3k • written 3 days ago by • 0
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 1 day ago by • 0
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110
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Different Shrunk Log2FC according with reference
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 20
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 2 days ago by 41k • written 2 days ago by ▴ 40
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by 41k • written 4.6 years ago by ▴ 10
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 days ago • updated 6 days ago lonn • 0
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How to retrieve detailed regression results from deseq2
DESeq2
15 days ago • updated 6 days ago Weiqian ▴ 10
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DESeq filtering specific to contrasts
DESeq2
updated 7 days ago by 41k • written 10 weeks ago by • 0
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5
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DESeq2 setting significant p-value
DESeq2
updated 7 days ago by 41k • written 5.0 years ago by ▴ 10
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DEG with low counts
DESeq2
updated 7 days ago by 41k • written 11 days ago by • 0
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rlog transformation
DESeq2
updated 8 days ago by 41k • written 8 days ago by • 0
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 days ago by 41k • written 8 days ago by • 0
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1
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115
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covariate with negative and positive values
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 30
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1
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 8 days ago by ★ 4.0k • written 9 days ago by • 0
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5
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 days ago by • 0 • written 10 months ago by • 0
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4
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 9 days ago by 41k • written 6 months ago by • 0
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 10 days ago by 41k • written 11 days ago by ▴ 20
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112
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Deseq2 Rlog transformation
DESeq2
updated 11 days ago by ★ 4.0k • written 12 days ago by • 0
1
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2
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171
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Design Matrix within group comparison more than two groups
DESeq2
14 days ago • updated 13 days ago hemantcnaik • 0
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119
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Bioinformatics student
Des DESeq2
updated 14 days ago by • 0 • written 14 days ago by • 0
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159
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DESeq2 gives an error and R crashes
DESeq2
15 days ago • updated 14 days ago Shefali • 0
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2
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197
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 16 days ago by 41k • written 21 days ago by ▴ 30
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1
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143
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 16 days ago by 41k • written 17 days ago by • 0
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225
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Regressing out batch effects
DESeq2
updated 16 days ago by 41k • written 22 days ago by • 0
0
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2
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148
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 21 days ago by 65k • written 21 days ago by • 0
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155
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DESeq2 - Missing values in count matrix
DESeq2
updated 22 days ago by 65k • written 22 days ago by • 0
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6
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 22 days ago by 41k • written 23 days ago by • 0
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2
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154
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
24 days ago • updated 23 days ago michelafrancesconi8 • 0
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139
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
24 days ago • updated 23 days ago Layal • 0
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4
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235
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 23 days ago by 41k • written 24 days ago by • 0
1
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8
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1.2k
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DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 25 days ago by ★ 13k • written 10 months ago by ▴ 10
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1
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144
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 28 days ago by 41k • written 28 days ago by • 0
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218
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
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3
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PCA of different bacterial species
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by ▴ 10
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412
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 4 weeks ago fr8712ca-s • 0
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1
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161
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collapseReplicates dimension error
DESeq2 Dese
updated 4 weeks ago by 41k • written 5 weeks ago by • 0
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
4 weeks ago Anita ▴ 10
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213
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
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3
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287
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 20
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3
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Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
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7
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681
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DESeq2 unable to handle large count values
DESeq2
updated 5 weeks ago by 41k • written 5 months ago by • 0
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1
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166
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Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2 ctsGE
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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134
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
50 results • Page 1 of 1
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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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