Showing : deseq2 • reset
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Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by 41k • written 3 days ago by ▴ 10
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6
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215
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 3 days ago by ★ 1.3k • written 4 days ago by ▴ 130
2
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3
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177
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by ★ 4.1k • written 3 days ago by • 0
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2
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108
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DESeq2 v1.35.0
DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
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2
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139
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Deseq2 and Normalization of RNA sequencing data
DESeq2
5 days ago • updated 4 days ago kcarey • 0
0
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3
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137
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
0
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1
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146
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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 5 days ago by ★ 4.1k • written 5 days ago by • 0
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3
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253
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
1
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1
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111
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
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2
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124
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
6 days ago • updated 3 days ago Aurora • 0
0
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1
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104
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
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1
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111
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putting my own expression data in deseq2
DESeq2
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
3
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3
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239
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 7 days ago by ★ 4.1k • written 8 days ago by ▴ 10
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2
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211
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PCA plot suggestions
DESeq2 PCAtools
updated 10 days ago by 41k • written 12 days ago by • 0
1
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3
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223
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 10 days ago by 41k • written 11 days ago by • 0
2
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9
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392
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 11 days ago by 65k • written 11 days ago by • 0
0
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1
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155
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 12 days ago by 41k • written 12 days ago by • 0
1
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3
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216
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Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by 41k • written 12 days ago by ▴ 20
1
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4
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333
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
12 days ago • updated 11 days ago winwater0928 • 0
3
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1
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315
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 13 days ago by 41k • written 13 days ago by ▴ 40
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8
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351
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 12 days ago by ★ 1.3k • written 13 days ago by • 0
3
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3
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229
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
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1
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139
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rlog transformation
DESeq2
updated 18 days ago by 41k • written 18 days ago by • 0
0
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1
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113
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 18 days ago by 41k • written 18 days ago by • 0
1
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2
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715
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 days ago • updated 10 days ago ussarizona ▴ 10
0
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1
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135
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covariate with negative and positive values
DESeq2
updated 18 days ago by 41k • written 20 days ago by • 0
0
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1
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150
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
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4
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240
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
19 days ago • updated 17 days ago lonn • 0
0
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3
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207
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by 41k • written 21 days ago by ▴ 20
1
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2
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245
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How to retrieve detailed regression results from deseq2
DESeq2
26 days ago • updated 17 days ago Weiqian ▴ 10
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4
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270
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DEG with low counts
DESeq2
updated 17 days ago by 41k • written 22 days ago by • 0
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1
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133
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Deseq2 Rlog transformation
DESeq2
updated 21 days ago by ★ 4.1k • written 23 days ago by • 0
1
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2
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197
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Design Matrix within group comparison more than two groups
DESeq2
24 days ago • updated 23 days ago hemantcnaik • 0
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1
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135
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Bioinformatics student
Des DESeq2
updated 24 days ago by • 0 • written 24 days ago by • 0
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1
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178
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DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago Shefali • 0
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2
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223
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 27 days ago by 41k • written 4 weeks ago by ▴ 30
0
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1
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165
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 27 days ago by 41k • written 27 days ago by • 0
0
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2
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249
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Regressing out batch effects
DESeq2
updated 27 days ago by 41k • written 4 weeks ago by • 0
1
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4
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481
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 5 days ago JKim • 0
0
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7
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423
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DESeq filtering specific to contrasts
DESeq2
updated 17 days ago by 41k • written 11 weeks ago by • 0
0
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4
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602
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 20 days ago by 41k • written 6 months ago by • 0
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 days ago by • 0 • written 10 months 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 6 days ago by • 0 • written 4.6 years ago by ▴ 10
2
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5
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754
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DESeq2 setting significant p-value
DESeq2
updated 17 days ago by 41k • written 5.0 years ago by ▴ 10
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 18 days ago by • 0 • written 8.8 years ago by ▴ 30
45 results • Page 1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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Scholar to Michael Love 41k
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