Showing : DESEQ2 • reset
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Effect size using likelihood ratio test in DESeq2
DESeq2
1 day ago jd348 • 0
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2
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152
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Correct way to make multiple comparisons on DESeq2?
DESeq DESeq2 R
17 days ago • updated 3 days ago jbnrodriguez • 0
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1
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141
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Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 7 days ago by 34k • written 8 days ago by • 0
2
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1
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112
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Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
updated 7 days ago by 34k • written 8 days ago by ▴ 10
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1
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65
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Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 8 days ago by 58k • written 8 days ago by • 0
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2
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139
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Log fold change interpretation of time series with Wald test
DESeq2
9 days ago • updated 1 day ago jd348 • 0
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1
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131
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RNA Seq - Venn Diagramm - display exclusively expressed genes
VennDetail DESeq2
updated 9 days ago by 34k • written 9 days ago by • 0
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7
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247
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small dimensions in the matrix of counts from smallRNA using DESEq2
matrix DESeq2 SmallRNA dimensions small
10 days ago andreia • 0
1
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3
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170
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Choosing an svalue threshold from apeglm shrunken results in DESeq2
apeglm DESeq2
updated 10 days ago by 34k • written 12 days ago by ▴ 20
3
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2
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145
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Sequencing depth before and aftr normalisation with DESEQ2 doesn't look as expected: Problem?
normalisation DESEQ2
updated 11 days ago by ▴ 850 • written 11 days ago by • 0
3
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7
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336
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Nanostringdiff - defining contrast values for blocking variables in glm
limma edgeR DESeq2 NanoStringDiff
updated 8 days ago by 58k • written 15 days ago by • 0
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65
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error: cannot execute 'f951': execvp: No such file or directory when downloading DESeq2 package
DESeq2
17 days ago Yihan • 0
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3
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116
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 17 days ago by 34k • written 18 days ago by • 0
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1
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70
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What does one-sided p-value in DESeq2 mean in biological terms?
one-sided nbinomWaldTest p-value meta-analysis DESeq2
updated 18 days ago by 34k • written 19 days ago by • 0
1
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6
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193
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DESeq2 design for paired samples
DESeq2 paired
updated 17 days ago by 34k • written 18 days ago by ▴ 10
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1
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86
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Help me do a gene enrichment analysis
DESeq2 topGO heatmaps
updated 18 days ago by ▴ 20 • written 18 days ago by • 0
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4
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113
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normalising Biological replicates for differential analysis
DESeq2 Rtudio
updated 19 days ago by ▴ 850 • written 19 days ago by • 0
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6
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214
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How to calculate dispersion DESeq2 - Step by Step
DGE DESeq2 Differential
24 days ago • updated 19 days ago Zeke Smith ▴ 10
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1
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69
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pairwise within sample
DESeq2 microbiome
updated 20 days ago by 34k • written 22 days ago by • 0
2
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8
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363
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How does the design formula affect dispersion estimate in DESeq2?
deseq2
updated 20 days ago by 34k • written 12 months ago by • 0
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128
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Different PCA results when using rlog and vst transformations
vsn DESeq2 rlog BatchEffect
updated 20 days ago by 34k • written 23 days ago by • 0
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5
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224
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Recalculated abundance data output table with DEseq2
DESeq2
updated 2 days ago by 34k • written 23 days ago by • 0
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2
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150
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log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
24 days ago • updated 22 days ago Claire • 0
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4
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389
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Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 3.5 years ago by • 0
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3
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121
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 20 days ago by 34k • written 24 days ago by • 0
2
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4
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148
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
24 days ago • updated 19 days ago khaveh ▴ 10
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1
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78
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Question about my design
DESeq2
updated 23 days ago by 34k • written 23 days ago by • 0
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1
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89
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 23 days ago by ▴ 830 • written 25 days ago by • 0
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7
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217
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DESEQ2 log2FC is not following Normalized read count
DESeq2
updated 20 days ago by 34k • written 26 days ago by • 0
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3
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171
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DESEQ PCA
DESeq2 miRNA
updated 25 days ago by ▴ 850 • written 4 weeks ago by • 0
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3
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119
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 17 days ago by 34k • written 27 days ago by • 0
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4
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146
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ylim and xlim in Enhanced Volcano
DESeq2 EnhancedVolcano Bioconductor
updated 27 days ago by 3.4k • written 27 days ago by • 0
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1
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139
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DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4 weeks ago by 34k • written 4 weeks ago by • 0
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1
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171
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How to write design and contrast in DESeq2 to find the up-regulated genes where the design have interactions
DESeq2
updated 4 weeks ago by 34k • written 4 weeks ago by • 0
1
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2
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113
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pairwise comparison + interaction term in DESeq2
DESeq2 interaction pairwise
4 weeks ago Lucas • 0
1
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4
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234
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weird MAplot or volcano plot of DESeq2 diff result
DESeq2
updated 4 weeks ago by 34k • written 5 weeks ago by ▴ 20
1
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5
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198
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lfcShrink probelm in many 0 count genes RNA-seq data
ashr DESeq2 apeglm
updated 20 days ago by 34k • written 4 weeks ago by ▴ 20
4
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9
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298
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DESeq2 paired design
DESeq2
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
1
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3
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168
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Not full rank DESeq2
DESeq2 DifferentialExpression
updated 5 weeks ago by 58k • written 5 weeks ago by • 0
1
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1
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98
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Different DESeq2 results
DESeq2 DifferentialExpression
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
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1
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87
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collided row names in heatmap.2
heatmap.2 genefilter deseq2
updated 5 weeks ago by 58k • written 5 weeks ago by • 0
2
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2
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174
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Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 5 weeks ago by 34k • written 5 weeks ago by • 0
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2
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109
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Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
5 weeks ago peter.zhouyu • 0
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4
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203
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Batch-corrected expression matrix NOT on a log2 scale
DESeq2 limma
updated 5 weeks ago by 3.4k • written 5 weeks ago by ▴ 60
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5
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217
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Incosistency between contrast and coef parameters in lfcShrink function
DESeq2
updated 5 weeks ago by 34k • written 6 weeks ago by • 0
3
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1
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152
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Compare two samples by Deseqs
DESeq2 RNASeq
updated 6 weeks ago by 3.4k • written 6 weeks ago by ▴ 10
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2
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124
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DESEQ2 - compensating quality difference in replicate samples
DESeq2
6 weeks ago Shail • 0
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5
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162
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Replicates in DESeq2
DESeq2
updated 23 days ago by 34k • written 6 weeks ago by • 0
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85
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Subject paired DESeq2 design
DESeq2 paired design
updated 6 weeks ago by 34k • written 6 weeks ago by ▴ 10
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2
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118
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Relative abundance of differentially abundant ASVs after DESeq2
DESeq2
6 weeks ago • updated 5 weeks ago Marion • 0
50 results • Page 1 of 1
Recent ...
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Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
Comment: Issue::DesignPrimers DECIPHER by slwmartin • 0
Hey, I'm having this issue too. I've tried reinstalling using Conda a few times without luck. Did you reinstall with Conda or from the tar …
Comment: Log fold change interpretation of time series with Wald test by jd348 • 0
So would you recommend still using Log2fold change as a measurement for effect size?
Votes
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
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