Showing : spatialexperiment • reset
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 9 months ago by ▴ 40 • written 10 months ago by • 0
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372
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
13 months ago Ibrahim • 0
0
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1
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693
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Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH SpatialExperiment
16 months ago Matthew Thornton ▴ 390
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990
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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
0
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589
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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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1.1k
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Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
21 months ago Peter Hickey ▴ 760
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1.3k
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Job: Bioinformatics Spatial Omics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
SpatialExperiment JobPosting
2.5 years ago Peter Hickey ▴ 760
1
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0
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2.8k
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Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.8 years ago cathalgking ▴ 10
0
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1
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1.4k
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cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 2.9 years ago by ▴ 160 • written 2.9 years ago by ▴ 10
9 results • Page 1 of 1
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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…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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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