Showing : scuttle • reset
2
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5
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768
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scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 3 months ago by ★ 28k • written 3 months ago by ▴ 10
2
votes
1
reply
680
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 11 months ago by ★ 4.7k • written 11 months ago by ★ 1.6k
0
votes
3
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1.7k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 18 months ago by ★ 4.7k • written 18 months ago by • 0
1
vote
0
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2.2k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.1 years ago cathalgking ▴ 10
0
votes
1
reply
1.0k
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 2.1 years ago by ▴ 160 • written 2.2 years ago by ▴ 10
2
votes
2
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1.7k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.0 years ago behr201 • 0
3
votes
3
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2.1k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.4 years ago enricoferrero ▴ 680
4
votes
5
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3.2k
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 680
5
votes
4
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7.7k
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scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 680
9 results • Page 1 of 1
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Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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