Showing: scater • reset
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differential expression between clusters (in distinct "treatments") in scRNAseq
limma scran scde scater sc3 written 6 days ago by Bogdan • 550
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emptyDrops result is full NAs
scran scater dropletutils scrna-seq written 15 days ago by hamza_karakurt • 30
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84
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scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater delayedarray biocsingular written 4 weeks ago by kevin.rue • 220 • updated 4 weeks ago by Aaron Lun • 24k
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176
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ERROR - Size factors should be positive real numbers (using normalize() function)
qc scran scater singlecellexperiment normalize written 11 weeks ago by kushshah • 10
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125
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Usage of doubletCells() function before or after the batch correction?
scran scater scrna-seq doubletcells written 10 weeks ago by hamza_karakurt • 30 • updated 10 weeks ago by Aaron Lun • 24k
2
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124
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Unable to change point size in plotExpression()
scater singlecellexperiment plotexpression plotting written 10 weeks ago by kushshah • 10 • updated 10 weeks ago by Aaron Lun • 24k
4
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138
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Using SC3 with batch corrected MNN values
scran scater sc3 scrna-seq batch correction written 11 weeks ago by hamza_karakurt • 30 • updated 11 weeks ago by Vladimir Kiselev • 150
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204
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Log2(RPKM) counts in Bioconductor
R rpkm expression scater calcaverage written 11 weeks ago by kushshah • 10 • updated 11 weeks ago by Aaron Lun • 24k
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166
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Dunn Index for Clusters from scRNA-Seq
clustering scran scater scrna-seq dunn index written 3 months ago by hamza_karakurt • 30 • updated 3 months ago by Aaron Lun • 24k
2
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154
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Modularity values of clusters and Differential Expression in scRNA-Seq
igraph scran scater scrna-seq rots written 3 months ago by hamza_karakurt • 30 • updated 3 months ago by Aaron Lun • 24k
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145
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Adding labels on clusters in a t-SNE plot and changing colors
ggplot2 rtsne scran scater scrna-seq written 4 months ago by hamza_karakurt • 30 • updated 4 months ago by Aaron Lun • 24k
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1
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149
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1
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scater error: invalid rownames length
scater written 4 months ago by lileijie1992 • 0 • updated 4 months ago by Aaron Lun • 24k
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132
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scran/scater Normalized matrix
scran normalized counts scater written 5 months ago by Radek • 60 • updated 5 months ago by Aaron Lun • 24k
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205
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scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater written 5 months ago by heyao • 30 • updated 5 months ago by Aaron Lun • 24k
2
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1
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229
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Gene ID to Gene Name/Symbol in loom files
scater loomr scopeloomr written 6 months ago by Abhishek Singh • 20 • updated 6 months ago by Aaron Lun • 24k
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305
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Deconvolution Method in Seurat and convert from SingleCellExperiment
rnaseq scater seurat singlecellexperiment written 6 months ago by hamza_karakurt • 30 • updated 6 months ago by Gordon Smyth ♦ 37k
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How to resolve these trendVar() warnings and errors
scran scater singlecellexperiment written 6 months ago by Abhishek Singh • 20 • updated 6 months ago by Aaron Lun • 24k
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1
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194
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Top variable features used by 'runPCA' in scater
pca scater features written 6 months ago by jws • 0 • updated 6 months ago by Aaron Lun • 24k
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1
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195
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plotPlatePosition and plate_position
R scater singlecellexperiment written 6 months ago by TJ • 0 • updated 6 months ago by Aaron Lun • 24k
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1
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282
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1
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Problem installing scater
R bioconductor scater biocmanager written 6 months ago by hfberg • 0 • updated 6 months ago by Aaron Lun • 24k
2
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1
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213
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1
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Change the number of clusters with scater
clustering scran scater scrnaseq written 7 months ago by shbrief • 10 • updated 7 months ago by Aaron Lun • 24k
1
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1
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475
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newSCESet and SingleCellExperiment basic differences and TMM Normalization
rnaseq single-cell scater seurat singlecellexperiment written 8 months ago by hamza_karakurt • 30
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416
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Scater package PlotExpression
scater written 10 months ago by mayank.geit89 • 0
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1
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213
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RNAseq scater error in plotQC()
scater scrnaseq plotqc written 11 months ago by Vladimir Krasikov • 90 • updated 11 months ago by Aaron Lun • 24k
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rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scran single-cell scater written 13 months ago by MengChun Tseng • 10 • updated 12 months ago by Martin Morgan ♦♦ 23k
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