Showing : DESeq2 • reset
5
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14
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2.1k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 14 hours ago by • 0 • written 4.6 years ago by ▴ 10
9
votes
12
replies
7.7k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 1 day ago by • 0 • written 8.8 years ago by ▴ 30
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 19 days ago by ★ 13k • written 9 months ago by ▴ 10
0
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7
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398
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DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 24 days ago fr8712ca-s • 0
0
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7
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352
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DESeq filtering specific to contrasts
DESeq2
updated 13 hours ago by 41k • written 9 weeks ago by • 0
1
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6
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393
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 16 days ago by 41k • written 16 days ago by • 0
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 2 days ago by • 0 • written 10 months ago by • 0
2
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5
replies
666
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DESeq2 setting significant p-value
DESeq2
updated 15 hours ago by 41k • written 5.0 years ago by ▴ 10
0
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4
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219
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 17 days ago by 41k • written 18 days ago by • 0
0
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4
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199
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DEG with low counts
DESeq2
updated 18 hours ago by 41k • written 5 days ago by • 0
0
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4
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556
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 3 days ago by 41k • written 5 months ago by • 0
2
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3
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315
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PCA of different bacterial species
DESeq2
updated 23 days ago by 41k • written 24 days ago by ▴ 10
0
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3
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146
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 3 days ago by 41k • written 4 days ago by ▴ 20
0
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3
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112
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
updated 22 hours ago by ★ 4.0k • written 2 days ago by • 0
0
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2
replies
200
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago • updated 29 days ago kcarey • 0
0
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2
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215
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Regressing out batch effects
DESeq2
updated 10 days ago by 41k • written 15 days ago by • 0
1
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2
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199
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
29 days ago • updated 23 days ago Chanderkant Chaudhary • 0
3
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2
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190
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
25 days ago Anita ▴ 10
0
votes
2
replies
133
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 14 days ago by 65k • written 14 days ago by • 0
1
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2
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156
views
Design Matrix within group comparison more than two groups
DESeq2
7 days ago • updated 6 days ago hemantcnaik • 0
0
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2
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143
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
17 days ago • updated 16 days ago michelafrancesconi8 • 0
0
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2
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183
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 10 days ago by 41k • written 14 days ago by ▴ 30
1
vote
2
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192
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How to retrieve detailed regression results from deseq2
DESeq2
9 days ago • updated 10 hours ago Weiqian ▴ 10
1
vote
1
reply
130
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
17 days ago • updated 16 days ago Layal • 0
0
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1
reply
135
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 22 days ago by 41k • written 22 days ago by • 0
0
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1
reply
61
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
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111
views
Bioinformatics student
Des DESeq2
updated 7 days ago by • 0 • written 7 days ago by • 0
0
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1
reply
79
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 1 day ago by ★ 4.0k • written 2 days ago by • 0
0
votes
1
reply
149
views
collapseReplicates dimension error
DESeq2 Dese
updated 25 days ago by 41k • written 28 days ago by • 0
1
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1
reply
149
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DESeq2 - Missing values in count matrix
DESeq2
updated 15 days ago by 65k • written 15 days ago by • 0
0
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1
reply
101
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Deseq2 Rlog transformation
DESeq2
updated 4 days ago by ★ 4.0k • written 6 days ago by • 0
0
votes
1
reply
131
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 10 days ago by 41k • written 10 days ago by • 0
0
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1
reply
145
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DESeq2 gives an error and R crashes
DESeq2
9 days ago • updated 8 days ago Shefali • 0
0
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1
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79
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covariate with negative and positive values
DESeq2
updated 1 day ago by 41k • written 3 days ago by • 0
0
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1
reply
56
views
rlog transformation
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
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1
reply
52
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 1 day ago by 41k • written 1 day ago by • 0
36 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
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Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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