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2
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5
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1.2k
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 13 months ago by ★ 29k • written 13 months ago by ▴ 10
2
votes
1
reply
1.1k
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 21 months ago by ★ 5.0k • written 22 months ago by ★ 1.6k
0
votes
3
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2.2k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
0
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2.9k
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Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.9 years ago cathalgking ▴ 10
0
votes
1
reply
1.4k
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 3.0 years ago by ▴ 160 • written 3.0 years ago by ▴ 10
2
votes
2
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2.3k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.9 years ago behr201 • 0
3
votes
3
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2.7k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.2 years ago enricoferrero ▴ 680
4
votes
5
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4.0k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 680
5
votes
4
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9.1k
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scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 680
9 results • Page 1 of 1
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Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results by sup0903 • 0
This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Comment: Ensembl site unresponsive via biomaRt by sebastianenewell • 0
> I think this is an unrelated issue. The original post includes the > message Error: 'curl_parse_url' is not an exported object from > 'na…
Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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