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Job:
Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting
CuratedAtlasQueryR
MoleculeExperiment
SingleCellExperiment
SpatialExperiment
17 months ago
Stefano Mangiola
▴ 40
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591
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News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
19 months ago
info
▴ 10
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DESeq with multiple condition
MoleculeExperiment
DifferentialExpression
DESeq2
updated 23 months ago by
ATpoint
★ 5.0k • written 23 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 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
irenekokosaikia
• 0
4 results • Page
1 of 1
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Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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