Showing : scater • reset
8
votes
4
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2.3k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
7
votes
5
replies
1.6k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
7
votes
3
replies
3.3k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF scater
3.6 years ago lirongrossmann ▴ 40
5
votes
2
replies
5.9k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment sc3 scater
updated 6.5 years ago by ▴ 150 • written 6.5 years ago by ▴ 10
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 660
5
votes
2
replies
1.7k
views
Accessing normalized counts
splatter singlecellexperiment scater
6.1 years ago luke.zappia ▴ 50
5
votes
6
replies
2.7k
views
Error when merging SCESet objects
scater single-cell
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
5
votes
4
replies
1.6k
views
scater runUMAP
scater runUMAP
2.1 years ago jianhai.zhang • 0
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
4
votes
3
replies
1.9k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ★ 1.5k
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 20
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
4
votes
0
replies
3.4k
views
Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
7.7 years ago Aaron Lun ★ 28k
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
4
votes
7
replies
6.3k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel scater
updated 6.9 years ago by ▴ 40 • written 7.0 years ago by • 0
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.1 years ago by ▴ 150 • written 5.1 years ago by ▴ 50
3
votes
3
replies
7.1k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 5.9 years ago by 25k • written 6.0 years ago by ▴ 10
3
votes
5
replies
1.3k
views
plotPlatePosition and plate_position
scater R singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
3
votes
3
replies
374
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
3
votes
4
replies
1.8k
views
Scran normalization error with computeSumFactors
scran scater
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
3
votes
9
replies
4.1k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
3
votes
2
replies
1.7k
views
FeaturePlot in scater
scater OSCA
22 months ago Guandong Shang ▴ 40
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
3
votes
3
replies
404
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 6 weeks ago by ▴ 160 • written 6 weeks ago by • 0
3
votes
2
replies
2.2k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.3 years ago • updated 3.2 years ago camerond • 0
3
votes
2
replies
3.1k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater simpleSingleCell workflows
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 70
3
votes
3
replies
2.4k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 3.5 years ago by ★ 28k • written 3.6 years ago by ▴ 60
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 6.5 years ago by ▴ 90 • written 6.5 years ago by • 0
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
3
votes
3
replies
2.7k
views
Gene ID to Gene Name/Symbol in loom files
Scater LoomR SCopeloomR
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
2
votes
7
replies
2.6k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
2
votes
5
replies
1.9k
views
sc3_prepare function error
sc3 scater single-cell single cell
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ★ 1.5k
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 20
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
2
replies
1.4k
views
scater error: invalid rownames length
scater
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
2
votes
5
replies
3.8k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 20 months ago by ▴ 60 • written 5.2 years ago by ▴ 50
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
2
votes
4
replies
3.6k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.1 years ago by • 0 • written 5.1 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
2
votes
1
reply
1.2k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 350
2
votes
1
reply
2.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
2
votes
4
replies
2.3k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.3 years ago by • 0 • written 4.1 years ago by • 0
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ★ 4.1k
2
votes
3
replies
1.3k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.2 years ago by ▴ 160 • written 3.2 years ago by • 0
2
votes
2
replies
1.3k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA BPPARAM scater BiocParallel runPCA
2.9 years ago doliv071 • 0
2
votes
3
replies
1.2k
views
scater::plotHeatmap with swap_rownames gives error
scater
2.5 years ago enricoferrero ▴ 660
2
votes
1
reply
237
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by ★ 1.5k
2
votes
7
replies
1.7k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 2.2 years ago by ▴ 270 • written 2.2 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by gene_bioconductor ▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
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Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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