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140
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scater cbind for singlecellexperiment objects problem
scater singlecellexperiment written 17 days ago by santos22903 • 0 • updated 17 days ago by Aaron Lun • 25k
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113
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could not find function "plotQC" in scater package
scater written 7 weeks ago by moldach • 20 • updated 7 weeks ago by Aaron Lun • 25k
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108
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Batch Corrections (MNN) with TPM values
rna-seq scran scater scrna-seq mnn written 8 weeks ago by hamza_karakurt • 30 • updated 8 weeks ago by Aaron Lun • 25k
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using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edger scran scater simplesinglecell written 4 months ago by Bogdan • 580 • updated 4 months ago by Aaron Lun • 25k
4
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207
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scRNA-seq : Classification of cell cycle phase
scran scater written 5 months ago by Bogdan • 580 • updated 5 months ago by Aaron Lun • 25k
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262
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scRNA-seq : runPCA() and denoisePCA()
scran scater written 5 months ago by Bogdan • 580 • updated 5 months ago by Aaron Lun • 25k
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159
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number of cell clusters in scRNA-seq
scran scater sc3 written 5 months ago by Bogdan • 580 • updated 5 months ago by Aaron Lun • 25k
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173
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differential expression between clusters (in distinct "treatments") in scRNAseq
limma scran scde scater sc3 written 5 months ago by Bogdan • 580
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emptyDrops result is full NAs
scran scater dropletutils scrna-seq written 6 months ago by hamza_karakurt • 30
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scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater delayedarray biocsingular written 6 months ago by kevin.rue • 230 • updated 6 months ago by Aaron Lun • 25k
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ERROR - Size factors should be positive real numbers (using normalize() function)
qc scran scater singlecellexperiment normalize written 8 months ago by kushshah • 10
4
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226
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Usage of doubletCells() function before or after the batch correction?
scran scater scrna-seq doubletcells written 8 months ago by hamza_karakurt • 30 • updated 8 months ago by Aaron Lun • 25k
2
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194
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Unable to change point size in plotExpression()
scater singlecellexperiment plotexpression plotting written 8 months ago by kushshah • 10 • updated 8 months ago by Aaron Lun • 25k
4
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294
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Using SC3 with batch corrected MNN values
scran scater sc3 scrna-seq batch correction written 8 months ago by hamza_karakurt • 30 • updated 8 months ago by Vladimir Kiselev • 150
6
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Log2(RPKM) counts in Bioconductor
R rpkm expression scater calcaverage written 8 months ago by kushshah • 10 • updated 8 months ago by Aaron Lun • 25k
1
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1
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261
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Dunn Index for Clusters from scRNA-Seq
clustering scran scater scrna-seq dunn index written 9 months ago by hamza_karakurt • 30 • updated 9 months ago by Aaron Lun • 25k
2
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245
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Modularity values of clusters and Differential Expression in scRNA-Seq
igraph scran scater scrna-seq rots written 9 months ago by hamza_karakurt • 30 • updated 9 months ago by Aaron Lun • 25k
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Adding labels on clusters in a t-SNE plot and changing colors
ggplot2 rtsne scran scater scrna-seq written 9 months ago by hamza_karakurt • 30 • updated 9 months ago by Aaron Lun • 25k
2
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268
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scater error: invalid rownames length
scater written 9 months ago by lileijie1992 • 0 • updated 9 months ago by Aaron Lun • 25k
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206
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scran/scater Normalized matrix
scran normalized counts scater written 11 months ago by Radek • 60 • updated 11 months ago by Aaron Lun • 25k
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334
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scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater written 11 months ago by heyao • 30 • updated 11 months ago by Aaron Lun • 25k
2
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1
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404
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Gene ID to Gene Name/Symbol in loom files
scater loomr scopeloomr written 11 months ago by Abhishek Singh • 20 • updated 11 months ago by Aaron Lun • 25k
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504
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Deconvolution Method in Seurat and convert from SingleCellExperiment
rnaseq scater seurat singlecellexperiment written 12 months ago by hamza_karakurt • 30 • updated 12 months ago by Gordon Smyth ♦ 39k
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How to resolve these trendVar() warnings and errors
scran scater singlecellexperiment written 12 months ago by Abhishek Singh • 20 • updated 12 months ago by Aaron Lun • 25k
2
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Top variable features used by 'runPCA' in scater
pca scater features written 12 months ago by jws • 0 • updated 12 months ago by Aaron Lun • 25k
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