Showing : SingleCellExperiment • reset
4
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15
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3.9k
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Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
3
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5
replies
5.5k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R bioconductor singlecellexperiment single cell
updated 6.5 years ago by • 0 • written 6.5 years ago by ▴ 10
2
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3
replies
1.6k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 15 months ago by ▴ 10 • written 5.2 years ago by ▴ 10
0
votes
2
replies
3.9k
views
problems when working with SingleCellExperiment object in scater
scater SingleCellExperiment
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by ▴ 10
1
vote
5
replies
823
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
5
votes
2
replies
5.8k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment sc3 scater
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 10
2
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2
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9.0k
views
Error: In seq_len(ncol(assay)) : first element used of 'length.out' argument
singlecellexperiment
6.2 years ago Marina V.V. • 0
4
votes
6
replies
535
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
3 months ago Dario Strbenac ★ 1.5k
0
votes
4
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1.3k
views
marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 40
4
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5
replies
2.2k
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
1
vote
3
replies
1.1k
views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
0
votes
1
reply
2.4k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 50
4
votes
7
replies
4.4k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
4
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6
replies
1.6k
views
How to best represent weights in SummarizedExperiment or SingleCellExperiment?
SummarizedExperiment SingleCellExperiment
updated 5.3 years ago by ▴ 950 • written 5.3 years ago by ▴ 100
4
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5
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1.5k
views
Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
ensembl cdschrom org.Hs.eg.db AnnotationDbi SingleCellExperiment
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 10
2
votes
1
reply
1.2k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
1
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3
replies
1.8k
views
Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
written 5.0 years ago by ▴ 350
2
votes
4
replies
3.5k
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 5.0 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
0
votes
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.4 years ago albadrs.93 ▴ 10
0
votes
1
reply
980
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
0
votes
2
replies
1.1k
views
Can't Load SingleCellExperiment Object
software error SingleCellExperiment
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
2
votes
4
replies
2.3k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.2 years ago by • 0 • written 4.1 years ago by • 0
0
votes
1
reply
1.2k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
1
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2
replies
1.8k
views
ident function in sce
SingleCellExperiment cluster identities sce
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
votes
3
replies
1.9k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
1
vote
1
reply
1.2k
views
Biological replicates in single cell experiments DE
singleCellExperiment
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
0
votes
6
replies
2.6k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 80
2
votes
7
replies
2.5k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.4 years ago by ★ 28k • written 3.5 years ago by ▴ 40
0
votes
1
reply
819
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 40
1
vote
2
replies
2.0k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.4 years ago lirongrossmann ▴ 40
0
votes
2
replies
1.4k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.4 years ago • updated 3.3 years ago jirkanov • 0
1
vote
3
replies
1.5k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.3 years ago achaillon • 0
1
vote
3
replies
1.0k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 3.3 years ago by ▴ 70 • written 3.3 years ago by • 0
2
votes
4
replies
885
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
19 months ago Romina • 0
1
vote
1
reply
941
views
counts method is not exported
singlecellexperiment
6.6 years ago Vladimir Kiselev ▴ 150
3
votes
3
replies
2.4k
views
Cannot create SingleCellExperiment object
singlecellexperiment
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 40
1
vote
2
replies
1.8k
views
SingleCellExperiment object cannot be used by Scater package?
scater singlecellexperiment simplesinglecell
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
5
votes
2
replies
1.6k
views
Accessing normalized counts
splatter singlecellexperiment scater
6.0 years ago luke.zappia ▴ 50
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
vote
5
replies
2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
5.5 years ago hamza_karakurt ▴ 50
7
votes
2
replies
2.3k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment dropletutils simplesinglecell
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 740
3
votes
2
replies
1.6k
views
Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment single-cell rnaseq
updated 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 50
3
votes
5
replies
1.2k
views
plotPlatePosition and plate_position
scater R singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
3
replies
1.5k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
19 months ago • updated 18 months ago merv ▴ 120
2
votes
2
replies
760
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
19 months ago k1m ▴ 20
0
votes
1
reply
708
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
votes
2
replies
866
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
9 months ago Matvii Mykhailichenko • 0
0
votes
1
reply
979
views
Rename colData column
SingleCellExperiment colData rename
updated 14 months ago by ▴ 770 • written 14 months ago by ▴ 10
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 20 months ago by 65k • written 20 months ago by ▴ 10
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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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