Showing : SingleCellExperiment • reset
1
vote
1
reply
177
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 11 days ago by ▴ 750 • written 15 days ago by • 0
0
votes
0
replies
122
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
3 months ago Ibrahim • 0
0
votes
0
replies
189
views
News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
3 months ago info ▴ 10
2
votes
2
replies
483
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 4 months ago by ▴ 10
1
vote
1
reply
893
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 5 months ago by ★ 28k • written 5 months ago by • 0
0
votes
1
reply
356
views
T cell subtype annotation
SingleCellExperiment
updated 6 months ago by 67k • written 6 months ago by • 0
0
votes
1
reply
1.4k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
0
replies
569
views
Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
7 months ago Stefano Mangiola ▴ 20
0
votes
4
replies
679
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
7 months ago vohara4 • 0
4
votes
1
reply
1.2k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 12 months ago by 67k • written 12 months ago by ▴ 20
4
votes
6
replies
1.1k
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
12 months ago Dario Strbenac ★ 1.5k
0
votes
0
replies
365
views
rpk per cell saved in SCE object.
SingleCellExperiment
12 months ago JalapenoCornbread • 0
1
vote
2
replies
1.4k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
13 months ago elgomez • 0
0
votes
7
replies
2.1k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 14 months ago by • 0
0
votes
1
reply
812
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 16 months ago by • 0
2
votes
5
replies
1.4k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
18 months ago • updated 17 months ago duez.tolga • 0
0
votes
2
replies
1.6k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
19 months ago Matvii Mykhailichenko • 0
0
votes
2
replies
1.4k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
19 months ago Lluís Revilla Sancho ▴ 760
1
vote
3
replies
3.1k
views
Remove certain highly expressing cells from a SCE
SingleCellExperiment
21 months ago mollyab12 • 0
0
votes
1
reply
1.6k
views
Rename colData column
SingleCellExperiment colData rename
updated 23 months ago by ▴ 780 • written 23 months ago by ▴ 10
2
votes
3
replies
2.1k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.0 years ago by ▴ 20 • written 6.0 years ago by ▴ 10
2
votes
3
replies
2.2k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.4 years ago • updated 2.3 years ago merv ▴ 140
2
votes
2
replies
1.1k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.4 years ago k1m ▴ 20
2
votes
4
replies
1.2k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.4 years ago Romina • 0
1
vote
1
reply
1.7k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.4 years ago by ▴ 750 • written 2.4 years ago by ▴ 140
5
votes
1
reply
3.5k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.4 years ago merv ▴ 140
0
votes
0
replies
1.4k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.4 years ago merv ▴ 140
4
votes
3
replies
2.2k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.5 years ago by 67k • written 2.5 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Use of Scater for QC in scRNA-seq: How to remove cells with less than certain number of genes supported with certain number of reads
SingleCellExperiment
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
2
votes
5
replies
5.5k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 23 months ago by • 0 • written 2.8 years ago by ▴ 10
2
votes
1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
1
vote
2
replies
1.2k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.0 years ago • updated 2.9 years ago msn ▴ 10
0
votes
1
reply
896
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
2
votes
2
replies
1.5k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.1 years ago by ★ 4.6k • written 3.1 years ago by ▴ 40
0
votes
0
replies
805
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.2 years ago Núria • 0
1
vote
2
replies
1.1k
views
Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
3.2 years ago Fatima • 0
3
votes
3
replies
2.1k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.3 years ago enricoferrero ▴ 680
0
votes
1
reply
3.3k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.4 years ago by ★ 4.6k • written 3.5 years ago by • 0
2
votes
5
replies
5.9k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.7 years ago by ▴ 60 • written 3.8 years ago by ▴ 20
2
votes
3
replies
1.7k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.0 years ago by ▴ 160 • written 4.0 years ago by • 0
3
votes
2
replies
2.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.0 years ago camerond • 0
0
votes
7
replies
2.6k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.0 years ago bge • 0
1
vote
3
replies
2.2k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
4
votes
5
replies
3.0k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 680
0
votes
2
replies
1.6k
views
from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.1 years ago achaillon • 0
1
vote
3
replies
1.3k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.1 years ago by ▴ 70 • written 4.1 years ago by • 0
2
votes
3
replies
2.0k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.1 years ago achaillon • 0
0
votes
2
replies
1.7k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.1 years ago jirkanov • 0
2
votes
2
replies
2.6k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.2 years ago lirongrossmann ▴ 50
0
votes
1
reply
1.1k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
Awards • All
Teacher to Axel Klenk ★ 1.1k
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to bastien_chassagnol • 0
Popular Question to Maria Doyle ▴ 100
Locations • All
Bangladesh, 24 minutes ago
The city by the bay, 54 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
United Arab Emirates, 6 hours ago
United States, 6 hours ago
Traffic: 622 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