Showing : DESeq2 • reset
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 2 hours ago by 41k • written 5 hours ago by • 0
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73
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Different Shrunk Log2FC according with reference
DESeq2
updated 10 hours ago by 41k • written 14 hours ago by ▴ 20
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 6 hours ago by ★ 1.3k • written 15 hours ago by • 0
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151
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 21 hours ago by 41k • written 1 day ago by ▴ 40
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4
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118
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 hours ago by ★ 1.3k • written 1 day ago by • 0
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145
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
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87
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rlog transformation
DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
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85
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 6 days ago by • 0
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95
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
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110
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covariate with negative and positive values
DESeq2
updated 6 days ago by 41k • written 8 days ago by • 0
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112
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 6 days ago by ★ 4.0k • written 7 days ago by • 0
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 4 days ago lonn • 0
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3
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173
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 20
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217
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How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago Weiqian ▴ 10
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229
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DEG with low counts
DESeq2
updated 5 days ago by 41k • written 10 days ago by • 0
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109
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Deseq2 Rlog transformation
DESeq2
updated 9 days ago by ★ 4.0k • written 10 days ago by • 0
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163
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Design Matrix within group comparison more than two groups
DESeq2
12 days ago • updated 11 days ago hemantcnaik • 0
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116
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Bioinformatics student
Des DESeq2
updated 12 days ago by • 0 • written 12 days ago by • 0
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154
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DESeq2 gives an error and R crashes
DESeq2
13 days ago Shefali • 0
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192
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 14 days ago by 41k • written 19 days ago by ▴ 30
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137
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 14 days ago by 41k • written 15 days ago by • 0
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219
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Regressing out batch effects
DESeq2
updated 14 days ago by 41k • written 20 days ago by • 0
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142
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
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152
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DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by 65k • written 20 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 20 days ago by 41k • written 21 days ago by • 0
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135
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago Layal • 0
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150
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
22 days ago • updated 21 days ago michelafrancesconi8 • 0
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229
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
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141
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by 41k • written 27 days ago by • 0
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324
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PCA of different bacterial species
DESeq2
updated 28 days ago by 41k • written 29 days ago by ▴ 10
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157
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collapseReplicates dimension error
DESeq2 Dese
updated 29 days ago by 41k • written 4 weeks ago by • 0
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199
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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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211
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
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210
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 4 weeks ago by 41k • written 5 weeks ago by ▴ 20
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243
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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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163
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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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132
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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164
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lfcShrink error: the line search routine failed
apeglm DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
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206
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
5 weeks ago feather-W • 0
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299
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
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4
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405
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DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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406
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DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago fr8712ca-s • 0
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236
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
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205
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i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
2
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233
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Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
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195
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Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
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3
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358
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
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320
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DESeq2: Comparing A Knockout to a Strain
DESeq2
6 weeks ago Viktor Thiel • 0
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206
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DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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