Showing : deseq2 • reset
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DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 3 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 5 days ago by • 0 • written 4.6 years ago by ▴ 10
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6
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201
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 2 days ago by ★ 1.3k • written 3 days ago by ▴ 130
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12
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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
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4
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269
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DEG with low counts
DESeq2
updated 17 days ago by 41k • written 21 days ago by • 0
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1
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164
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 26 days ago by 41k • written 26 days ago by • 0
2
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5
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751
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DESeq2 setting significant p-value
DESeq2
updated 17 days ago by 41k • written 5.0 years ago by ▴ 10
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7
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423
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DESeq filtering specific to contrasts
DESeq2
updated 16 days ago by 41k • written 11 weeks ago by • 0
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1
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133
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covariate with negative and positive values
DESeq2
updated 17 days ago by 41k • written 19 days ago by • 0
1
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2
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243
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How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago Weiqian ▴ 10
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1
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106
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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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220
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 26 days ago by 41k • written 4 weeks ago by ▴ 30
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3
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247
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
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1
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136
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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 4 days ago by ★ 4.1k • written 4 days ago by • 0
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2
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131
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Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago kcarey • 0
0
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1
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148
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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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2
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712
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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
1
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1
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88
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Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 10
0
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1
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112
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 days ago by 41k • written 18 days ago by • 0
0
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1
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136
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rlog transformation
DESeq2
updated 17 days ago by 41k • written 18 days ago by • 0
2
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3
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161
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
0
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2
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247
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Regressing out batch effects
DESeq2
updated 26 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 19 days ago by • 0 • written 10 months ago by • 0
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3
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48
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Couldn't connect to server while using "pathways"
DESeq2
updated 10 minutes ago by 65k • written 8 hours ago by • 0
3
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3
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227
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by 41k • written 13 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 19 days ago by 41k • written 6 months ago by • 0
1
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4
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479
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 4 days ago JKim • 0
3
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1
reply
313
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by 41k • written 12 days ago by ▴ 40
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4
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325
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
12 days ago • updated 10 days ago winwater0928 • 0
1
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3
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214
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Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by 41k • written 12 days ago by ▴ 20
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1
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154
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 days ago by 41k • written 11 days ago by • 0
0
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2
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208
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PCA plot suggestions
DESeq2 PCAtools
updated 9 days ago by 41k • written 11 days ago by • 0
2
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9
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390
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 11 days ago by • 0
0
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1
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132
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Bioinformatics student
Des DESeq2
updated 23 days ago by • 0 • written 24 days ago by • 0
1
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3
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217
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 10 days ago by 41k • written 10 days ago by • 0
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3
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205
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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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196
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Design Matrix within group comparison more than two groups
DESeq2
23 days ago hemantcnaik • 0
3
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3
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228
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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 7 days ago by ▴ 10
0
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1
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101
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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 6 days ago by • 0
0
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2
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120
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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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106
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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
0
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1
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176
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DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago Shefali • 0
0
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8
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346
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 days ago by ★ 1.3k • written 12 days ago by • 0
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4
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237
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
19 days ago • updated 16 days ago lonn • 0
0
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3
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132
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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 4 days ago by • 0
0
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1
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131
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Deseq2 Rlog transformation
DESeq2
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
46 results • Page 1 of 1
Recent ...
Replies
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
btw that was run on M1 mac
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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