Showing : DESeq2 • reset
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DESeq2 v1.35.0
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
6
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19
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2.5k
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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 days ago by • 0 • written 4.6 years ago by ▴ 10
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6
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179
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 1 day ago by ★ 1.3k • written 2 days ago by ▴ 130
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12
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 17 days ago by • 0 • written 8.8 years ago by ▴ 30
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4
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268
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DEG with low counts
DESeq2
updated 16 days ago by 41k • written 20 days ago by • 0
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1
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162
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 25 days ago by 41k • written 25 days ago by • 0
2
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5
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744
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DESeq2 setting significant p-value
DESeq2
updated 16 days ago by 41k • written 5.0 years ago by ▴ 10
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7
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421
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DESeq filtering specific to contrasts
DESeq2
updated 15 days ago by 41k • written 11 weeks ago by • 0
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133
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covariate with negative and positive values
DESeq2
updated 16 days ago by 41k • written 18 days ago by • 0
1
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2
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241
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How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago Weiqian ▴ 10
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1
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101
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
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2
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219
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 25 days ago by 41k • written 4 weeks ago by ▴ 30
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3
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240
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
0
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1
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128
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
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2
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119
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Deseq2 and Normalization of RNA sequencing data
DESeq2
3 days ago • updated 2 days ago kcarey • 0
0
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1
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147
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
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2
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709
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago ussarizona ▴ 10
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1
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57
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Handling multiple differential expression comparisons
DESeq2
updated 3 hours ago by 41k • written 1 day ago by • 0
0
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1
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111
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 16 days ago by 41k • written 17 days ago by • 0
0
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1
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136
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rlog transformation
DESeq2
updated 16 days ago by 41k • written 17 days ago by • 0
2
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3
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136
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 hours ago by ★ 4.1k • written 1 day ago by • 0
0
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2
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245
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Regressing out batch effects
DESeq2
updated 25 days ago by 41k • written 4 weeks 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 18 days ago by • 0 • written 10 months ago by • 0
3
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3
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224
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by 41k • written 12 days ago by • 0
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4
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601
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 18 days ago by 41k • written 6 months ago by • 0
1
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4
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475
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 3 days ago JKim • 0
3
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1
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308
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 40
1
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4
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318
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago winwater0928 • 0
1
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3
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208
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Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
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150
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 10 days ago by 41k • written 10 days ago by • 0
0
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2
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203
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PCA plot suggestions
DESeq2 PCAtools
updated 8 days ago by 41k • written 10 days ago by • 0
2
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9
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384
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 days ago by 65k • written 10 days ago by • 0
0
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1
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132
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Bioinformatics student
Des DESeq2
updated 22 days ago by • 0 • written 23 days ago by • 0
1
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3
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213
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 days ago by 41k • written 9 days ago by • 0
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3
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204
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by 41k • written 20 days ago by ▴ 20
1
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2
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193
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Design Matrix within group comparison more than two groups
DESeq2
22 days ago hemantcnaik • 0
3
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3
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222
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 days ago by ★ 4.1k • written 6 days ago by ▴ 10
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1
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98
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
0
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2
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114
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
5 days ago • updated 2 days ago Aurora • 0
0
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1
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98
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putting my own expression data in deseq2
DESeq2
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
0
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1
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174
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DESeq2 gives an error and R crashes
DESeq2
24 days ago • updated 23 days ago Shefali • 0
0
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3
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122
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
0
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4
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235
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 days ago • updated 15 days ago lonn • 0
0
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1
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130
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Deseq2 Rlog transformation
DESeq2
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
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8
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341
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 days ago by ★ 1.3k • written 11 days ago by • 0
45 results • Page 1 of 1
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Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons by Michael Love 41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
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Print Differentially Expressed Exons From Dexseq Results
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
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