Showing : SingleCellExperiment • reset
2
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4
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
15 days ago • updated 1 day ago rohitsatyam102 ▴ 10
2
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3
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135
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3 months ago by ▴ 40 • written 3 months ago by • 0
3
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2
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144
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3 months ago camerond • 0
0
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7
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307
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3 months ago • updated 12 weeks ago bge • 0
1
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3
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174
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4 months ago by ★ 26k • written 4 months ago by • 0
2
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5
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224
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4 months ago by ★ 26k • written 4 months ago by ▴ 570
0
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2
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127
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4 months ago achaillon • 0
1
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3
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145
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singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4 months ago by ▴ 30 • written 4 months ago by • 0
1
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3
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190
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
5 months ago • updated 4 months ago achaillon • 0
0
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2
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196
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
5 months ago jirkanov • 0
1
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2
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163
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Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
5 months ago lirongrossmann ▴ 30
0
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1
reply
106
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 6 months ago by ★ 26k • written 6 months ago by ▴ 30
2
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2
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161
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How to run runNMF in parallel?
scater single SingleCellExperiment
6 months ago p.joshi ▴ 20
0
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6
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376
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 8 months ago by ★ 26k • written 8 months ago by ▴ 60
1
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1
reply
144
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Biological replicates in single cell experiments DE
singleCellExperiment
updated 8 months ago by ★ 26k • written 8 months ago by • 0
0
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4
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180
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marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 8 months ago by ★ 26k • written 8 months ago by ▴ 30
0
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0
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116
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Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
9 months ago lirongrossmann ▴ 60
0
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3
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327
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marker genes in singleR
singleR singlecell singlecellexperiment
updated 9 months ago by ★ 26k • written 9 months ago by ▴ 30
1
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2
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99
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ident function in sce
SingleCellExperiment cluster identities sce
updated 12 months ago by ★ 26k • written 12 months ago by • 0
0
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1
reply
98
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Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 12 months ago by ★ 26k • written 12 months ago by • 0
1
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4
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304
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Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3 months ago by • 0 • written 14 months ago by • 0
0
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2
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357
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Can't Load SingleCellExperiment Object
software error SingleCellExperiment
updated 17 months ago by ★ 26k • written 17 months ago by • 0
0
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1
reply
234
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scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 17 months ago by ★ 26k • written 17 months ago by • 0
0
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2
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258
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PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
18 months ago albadrs.93 ▴ 10
3
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2
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445
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single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 23 months ago by ★ 26k • written 23 months ago by • 0
2
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3
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1.2k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
2.1 years ago • updated 2.0 years ago kushshah ▴ 10
2
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3
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389
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Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 2.1 years ago by ★ 26k • written 2.1 years ago by ▴ 10
1
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2
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423
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Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
updated 2.1 years ago by ★ 26k • written 2.1 years ago by ▴ 330
2
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1
reply
272
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Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 2.1 years ago by ★ 26k • written 2.1 years ago by ▴ 10
4
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5
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455
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Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
ensembl cdschrom org.Hs.eg.db AnnotationDbi SingleCellExperiment
updated 2.1 years ago by 56k • written 2.1 years ago by ▴ 10
2
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2
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372
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.3 years ago by 25k • written 2.3 years ago by ▴ 10
4
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6
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444
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How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 2.3 years ago by ▴ 870 • written 2.3 years ago by ▴ 90
3
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7
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758
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removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 2.4 years ago by ★ 26k • written 2.4 years ago by • 0
0
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1
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937
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Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 2.4 years ago by 42k • written 2.4 years ago by ▴ 50
1
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3
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396
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How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 2.4 years ago by ★ 26k • written 2.4 years ago by ▴ 20
3
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5
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429
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plotPlatePosition and plate_position
scater R singlecellexperiment
updated 2.4 years ago by ★ 26k • written 2.4 years ago by • 0
3
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2
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702
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Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment single-cell rnaseq
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 50
2
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2
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590
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Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment dropletutils simplesinglecell
updated 2.6 years ago by ★ 26k • written 2.6 years ago by ▴ 460
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5
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newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
2.6 years ago hamza_karakurt ▴ 50
6
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12
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1.6k
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Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 2.9 years ago by ★ 26k • written 2.9 years ago by • 0
0
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1
reply
1.6k
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Conversion to SingleCellExperiment from Seurat objects
Seurat SingleCellExperiment
3.0 years ago Wolfgang Huber 13k
5
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2
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449
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Accessing normalized counts
splatter singlecellexperiment scater
3.1 years ago luke.zappia ▴ 50
4
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15
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1.9k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 3.2 years ago by ★ 26k • written 3.2 years ago by • 0
1
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2
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876
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SingleCellExperiment object cannot be used by Scater package?
scater singlecellexperiment simplesinglecell
updated 3.3 years ago by ★ 26k • written 3.3 years ago by • 0
2
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2
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4.8k
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Error: In seq_len(ncol(assay)) : first element used of 'length.out' argument
singlecellexperiment
3.3 years ago Marina V.V. • 0
5
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2
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2.8k
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Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment sc3 scater
updated 3.5 years ago by ▴ 150 • written 3.5 years ago by ▴ 10
3
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3
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1.3k
views
Cannot create SingleCellExperiment object
singlecellexperiment
updated 3.5 years ago by ★ 26k • written 3.5 years ago by ▴ 40
3
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5
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3.3k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R bioconductor singlecellexperiment single cell
updated 3.6 years ago by • 0 • written 3.6 years ago by ▴ 10
0
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2
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1.8k
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problems when working with SingleCellExperiment object in scater
scater SingleCellExperiment
updated 3.6 years ago by ▴ 90 • written 3.6 years ago by ▴ 10
1
vote
1
reply
543
views
counts method is not exported
singlecellexperiment
3.7 years ago Vladimir Kiselev ▴ 150
50 results • Page 1 of 1
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Comment: erorr in normalization with DiffBind: pv$binding[, colnum] <- pv$peaks[[i]]$RPKM by ben.vanderveer • 0
Thanks, it works! I did call the object in my script different, but for clarity here I changed it. best, Ben
Comment: phenotypic table for DESeqDataSetFromHTSeqCount by rbenel ▴ 20
Yea, no issue there... ``` FirstFile <- read.table(file.path(ExonCountFiles, sampleFiles)[1]) head(FirstFile) V1 V2 1 EN…
Comment: phenotypic table for DESeqDataSetFromHTSeqCount by Michael Love 33k
Another issue is whether R is allowed to read those files I guess. Try reading one in with `read.table` or `scan(..., what="char")`
Comment: phenotypic table for DESeqDataSetFromHTSeqCount by rbenel ▴ 20
Sorry the `directory` variable in my code was `ExonCountFiles` A vector of `TRUE` :) Which means to me that the function is looking for…
Answer: DESeq2 Multi-factor design not full rank by Michael Love 33k
> How can I create a custom model matrix that requires colData information from a dds object that in turn hasn’t been generated due to the …
Votes
Answer: erorr in normalization with DiffBind: pv$binding[, colnum] <- pv$peaks[[i]]$RPKM
Answer: phenotypic table for DESeqDataSetFromHTSeqCount
Comment: `aperm`, `realize`, `writeHDF5Array`, and `ReshapedHDF5Array` are block size awa
Answer: Error: C stack usage of HDF5Array
Answer: "dim<-" against on-disk arrays
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