Showing : DESeq2 • reset
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3
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63
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Couldn't connect to server while using "pathways"
DESeq2
updated 2 hours ago by 65k • written 9 hours ago by • 0
1
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1
reply
92
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Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 10
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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6
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202
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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
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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2
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133
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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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2
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99
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DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
0
votes
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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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
reply
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
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
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
1
vote
1
reply
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
0
votes
1
reply
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
votes
1
reply
107
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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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231
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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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2
replies
208
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PCA plot suggestions
DESeq2 PCAtools
updated 10 days ago by 41k • written 11 days ago by • 0
1
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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
vote
3
replies
217
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 10 days ago by 41k • written 10 days ago by • 0
1
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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
2
votes
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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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 13 days ago by • 0
0
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1
reply
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
1
vote
3
replies
214
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Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by 41k • written 12 days ago by ▴ 20
3
votes
1
reply
313
views
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
3
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3
replies
227
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
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
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
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
2
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5
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752
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DESeq2 setting significant p-value
DESeq2
updated 17 days ago by 41k • written 5.0 years ago by ▴ 10
0
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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
0
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1
reply
136
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rlog transformation
DESeq2
updated 18 days ago by 41k • written 18 days ago by • 0
0
votes
1
reply
112
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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
0
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1
reply
133
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covariate with negative and positive values
DESeq2
updated 18 days ago by 41k • written 19 days ago by • 0
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
0
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1
reply
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
2
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5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 days ago by • 0 • written 10 months ago by • 0
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
0
votes
3
replies
205
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by 41k • written 21 days ago by ▴ 20
0
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1
reply
131
views
Deseq2 Rlog transformation
DESeq2
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
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
24 days ago • updated 23 days ago hemantcnaik • 0
0
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1
reply
132
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Bioinformatics student
Des DESeq2
updated 24 days ago by • 0 • written 24 days ago by • 0
0
votes
1
reply
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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2
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221
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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
0
votes
1
reply
164
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 26 days ago by 41k • written 27 days ago by • 0
0
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2
replies
247
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Regressing out batch effects
DESeq2
updated 26 days ago by 41k • written 4 weeks ago by • 0
0
votes
2
replies
171
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
vote
1
reply
167
views
DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
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6
replies
434
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
2
replies
173
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
50 results • Page 1 of 1
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Replies
Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
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 …
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
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
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