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Job:
Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
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CuratedAtlasQueryR
MoleculeExperiment
SingleCellExperiment
SpatialExperiment
8 months ago
Stefano Mangiola
▴ 40
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News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
10 months ago
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DESeq with multiple condition
MoleculeExperiment
DifferentialExpression
DESeq2
updated 14 months ago by
ATpoint
★ 4.7k • written 14 months ago by
michelafrancesconi8
• 0
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Missing genes in the differentially expressed gene list which otherwise are expected to show expression post treatment.
MoleculeExperiment
updated 17 months ago by
ATpoint
★ 4.7k • written 17 months ago by
irenekokosaikia
• 0
4 results • Page
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Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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