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SpatialExperiment
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Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
2.1 years ago
cathalgking
▴ 10
0
votes
1
reply
1.0k
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cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 2.1 years ago by
alan.ocallaghan
▴ 160 • written 2.2 years ago by
cathalgking
▴ 10
0
votes
0
replies
999
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Job:
Bioinformatics Spatial Omics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
SpatialExperiment
JobPosting
21 months ago
Peter Hickey
▴ 750
0
votes
0
replies
685
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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
12 months ago
Peter Hickey
▴ 750
0
votes
0
replies
626
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Job:
Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting
CuratedAtlasQueryR
MoleculeExperiment
SingleCellExperiment
SpatialExperiment
9 months ago • updated 8 months ago
Stefano Mangiola
▴ 40
0
votes
1
reply
483
views
Basic import of seqFISH from Spatial Genomics genePS into SpatialExperiment
seqFISH
SpatialExperiment
7 months ago
Matthew Thornton
▴ 380
3
votes
2
replies
420
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment
SingleCellExperiment
SpatialFeatureExperiment
updated 17 days ago by
Stefano Mangiola
▴ 40 • written 8 weeks ago by
sarah.williams
• 0
0
votes
0
replies
406
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News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
10 months ago
info
▴ 10
0
votes
0
replies
154
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment
SingleCellExperiment
4 months ago
Ibrahim
• 0
9 results • Page
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome
by
James W. MacDonald
68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data
by
silickas
• 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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