Showing : singleCellExperiment • reset
4
votes
15
replies
4.0k
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 6.6 years ago by • 0 • written 6.6 years ago by ▴ 10
2
votes
3
replies
1.6k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 16 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
881
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 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
votes
2
replies
9.2k
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
593
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
4 months ago • updated 3 months ago Dario Strbenac ★ 1.5k
0
votes
4
replies
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 3.4 years ago by ★ 28k • written 3.4 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
2.5k
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 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
4
votes
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
1.6k
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
vote
3
replies
1.8k
views
Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
written 5.1 years ago by ▴ 360
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 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
0
votes
2
replies
1.2k
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
2.4k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.3 years ago by • 0 • written 4.2 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
vote
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 3.8 years ago by ★ 28k • written 3.8 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
841
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
1.5k
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
1.6k
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
933
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago Romina • 0
1
vote
1
reply
956
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 6.3 years ago by ★ 28k • written 6.3 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
3.7k
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
797
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
20 months ago k1m ▴ 20
0
votes
1
reply
723
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
939
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
0
votes
1
reply
1.1k
views
Rename colData column
SingleCellExperiment colData rename
updated 15 months ago by ▴ 780 • written 15 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
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
United States, 15 minutes ago
United States, 15 minutes ago
United States, 31 minutes ago
United States, 33 minutes ago
EMBL Heidelberg, 34 minutes ago
Traffic: 696 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6