Showing : DESeq2 • reset
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LRT, pairwise comparisons and p-value adjustment
DESeq2
17 hours ago boczniak767 ▴ 720
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3
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79
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Counter-directional LFC shrinkage
DESeq2
updated 10 hours ago by ★ 1.4k • written 21 hours ago by • 0
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2
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112
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 1 day ago by ★ 4.0k • written 3 days ago by • 0
0
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3
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140
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GSVA function
DESeq2 GSVA ssGSEA
updated 2 days ago by ★ 3.3k • written 4 days ago by • 0
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2
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113
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
5 days ago • updated 2 days ago sukeshinik5 • 0
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4
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240
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 3 days ago by ★ 4.2k • written 5 days ago by • 0
1
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8
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199
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
6 days ago boczniak767 ▴ 720
1
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3
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178
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 8 days ago by 66k • written 9 days ago by ▴ 720
2
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4
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257
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 8 days ago by 42k • written 11 days ago by • 0
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6
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632
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
12 days ago • updated 8 days ago Ken C • 0
4
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9
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338
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 12 days ago by ★ 4.2k • written 14 days ago by • 0
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3
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173
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 14 days ago by 42k • written 14 days ago by • 0
1
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2
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287
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
15 days ago • updated 12 days ago BioinfGuru ▴ 30
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8
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588
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 14 days ago by ▴ 30 • written 15 days ago by • 0
0
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1
reply
131
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 14 days ago by 42k • written 15 days ago by • 0
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1
reply
205
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 19 days ago by ★ 4.2k • written 19 days ago by • 0
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1
reply
127
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 20 days ago by ★ 4.2k • written 20 days ago by • 0
2
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7
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484
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
21 days ago • updated 18 days ago sajadahmad41454 • 0
2
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3
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284
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 24 days ago by ★ 4.2k • written 25 days ago by • 0
1
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1
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203
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Handling multiple differential expression comparisons
DESeq2
updated 24 days ago by 42k • written 25 days ago by ▴ 10
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6
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325
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 25 days ago by ★ 1.4k • written 26 days ago by ▴ 130
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2
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188
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DESeq2 v1.35.0
DESeq2
updated 26 days ago by 42k • written 26 days ago by • 0
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2
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227
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Deseq2 and Normalization of RNA sequencing data
DESeq2
27 days ago • updated 26 days ago kcarey • 0
0
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3
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252
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 27 days ago by ★ 4.2k • written 27 days ago by • 0
1
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3
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338
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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 21 days ago by ★ 4.2k • written 27 days ago by • 0
0
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3
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315
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 27 days ago by 42k • written 28 days ago by • 0
1
vote
1
reply
166
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
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1
reply
145
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putting my own expression data in deseq2
DESeq2
updated 29 days ago by ★ 4.2k • written 29 days ago by • 0
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2
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184
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
29 days ago • updated 26 days ago Aurora • 0
0
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1
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144
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
1
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4
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545
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DEseq2 coefficient
DESeq2 coefficient
3 months ago • updated 27 days ago JKim • 0
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2
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1.6k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 19 days ago by • 0 • written 16 months ago by ▴ 10
6
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19
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2.6k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 28 days ago by • 0 • written 4.7 years ago by ▴ 10
33 results • Page 1 of 1
Recent ...
Replies
Answer: Counter-directional LFC shrinkage by swbarnes2 ★ 1.4k
The y axes in those plots are logged. The average for condition1 is going to be higher than condition2 because of the very high outliers. …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contr…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…
Comment: Error in gseDO function by Guido Hooiveld ★ 4.0k
I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…
Comment: Counter-directional LFC shrinkage by ATpoint ★ 4.2k
Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.
Votes
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
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