Showing : SingleCellExperiment • reset
4
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15
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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
3
votes
5
replies
5.6k
views
SingleCellExperiment function in SingleCellExperiment package returns error (when reproducing example)
R bioconductor singlecellexperiment single cell
updated 6.5 years ago by • 0 • written 6.6 years ago by ▴ 10
2
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3
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1.6k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 15 months ago by ▴ 10 • written 5.3 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
856
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago • updated 8 months ago duez.tolga • 0
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
2
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2
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9.1k
views
Error: In seq_len(ncol(assay)) : first element used of 'length.out' argument
singlecellexperiment
6.3 years ago Marina V.V. • 0
4
votes
6
replies
571
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
3 months ago Dario Strbenac ★ 1.5k
0
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4
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1.3k
views
marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
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
1
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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
2.5k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 50
4
votes
7
replies
4.5k
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
votes
5
replies
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 5.1 years ago by 65k • written 5.1 years ago by ▴ 10
2
votes
1
reply
1.3k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment rpkm normalization qc
updated 5.1 years ago by ★ 28k • written 5.1 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 5.1 years ago by ▴ 350
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
0
votes
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.5 years ago albadrs.93 ▴ 10
0
votes
1
reply
1.0k
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 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
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
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
1.9k
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
2.0k
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 3.7 years ago by ★ 28k • written 3.7 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 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 80
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
0
votes
1
reply
833
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 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 jirkanov • 0
1
vote
3
replies
1.5k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.4 years ago achaillon • 0
1
vote
3
replies
1.0k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 3.4 years ago by ▴ 70 • written 3.4 years ago by • 0
2
votes
4
replies
917
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago Romina • 0
1
vote
1
reply
950
views
counts method is not exported
singlecellexperiment
6.7 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
1.7k
views
Accessing normalized counts
splatter singlecellexperiment scater
6.1 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 5.9 years ago by ★ 28k • written 5.9 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
5.6 years ago hamza_karakurt ▴ 50
7
votes
2
replies
2.4k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment dropletutils simplesinglecell
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 740
3
votes
2
replies
1.6k
views
Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment single-cell rnaseq
updated 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 50
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
2
votes
3
replies
1.6k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
20 months ago • updated 19 months ago merv ▴ 120
2
votes
2
replies
791
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
20 months ago k1m ▴ 20
0
votes
1
reply
718
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
votes
2
replies
904
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
0
votes
1
reply
1.0k
views
Rename colData column
SingleCellExperiment colData rename
updated 14 months ago by ▴ 780 • 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 21 months ago by 65k • written 21 months ago by ▴ 10
50 results • Page 1 of 1
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Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
btw that was run on M1 mac
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
the test is not portable > aa <- aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2") > str(aa) num [1:20, 1:20] 0.34 -0.0…
Comment: Method to find pathways different between 2 groups by Chris • 0
Sorry for not clear! Glad to know camera() is widely used. I just try to find papers use this method for learning purpose. Which gives more…
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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
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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