Showing : singlecellexperiment • reset
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
8 weeks ago Ibrahim • 0
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0
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150
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
10 weeks ago info ▴ 10
2
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2
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409
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 3 months ago by ▴ 10
1
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1
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723
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 4 months ago by ★ 28k • written 4 months ago by • 0
0
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1
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321
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T cell subtype annotation
SingleCellExperiment
updated 5 months ago by 67k • written 5 months ago by • 0
0
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1
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1.2k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 5 months ago by • 0 • written 6 months ago by • 0
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0
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523
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
6 months ago Stefano Mangiola ▴ 20
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4
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625
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
4
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1
reply
1.0k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 11 months ago by 67k • written 11 months ago by ▴ 20
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6
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1.0k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
11 months ago Dario Strbenac ★ 1.5k
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348
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rpk per cell saved in SCE object.
SingleCellExperiment
11 months ago JalapenoCornbread • 0
1
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2
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1.3k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
12 months ago elgomez • 0
0
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7
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2.0k
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Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 12 months ago by • 0
0
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1
reply
773
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 14 months ago by • 0
2
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5
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1.3k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
16 months ago duez.tolga • 0
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2
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1.5k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
18 months ago Matvii Mykhailichenko • 0
0
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2
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1.3k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
18 months ago Lluís Revilla Sancho ▴ 760
1
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3
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2.9k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
20 months ago • updated 19 months ago mollyab12 • 0
0
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1
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1.5k
views
Rename colData column
SingleCellExperiment colData rename
updated 22 months ago by ▴ 780 • written 22 months ago by ▴ 10
2
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3
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2.0k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 23 months ago by ▴ 20 • written 5.9 years ago by ▴ 10
2
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3
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2.1k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.3 years ago • updated 2.2 years ago merv ▴ 140
2
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2
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1.0k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.3 years ago k1m ▴ 20
2
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4
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1.2k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.3 years ago Romina • 0
1
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1
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1.6k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.3 years ago by ▴ 740 • written 2.3 years ago by ▴ 140
5
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1
reply
3.4k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.3 years ago merv ▴ 140
0
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0
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1.4k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.3 years ago merv ▴ 140
4
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3
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2.1k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 10
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1
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1.2k
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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 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
2
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5
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5.3k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 22 months ago by • 0 • written 2.7 years ago by ▴ 10
2
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1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
1
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2
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1.2k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.8 years ago msn ▴ 10
0
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1
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876
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.9 years ago by 67k • written 2.9 years ago by • 0
2
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2
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1.4k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.0 years ago by ★ 4.6k • written 3.0 years ago by ▴ 40
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0
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781
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.1 years ago Núria • 0
1
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2
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1.1k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
3.1 years ago Fatima • 0
3
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3
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2.0k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.2 years ago • updated 3.1 years ago enricoferrero ▴ 660
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1
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3.2k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by • 0
2
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5
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5.7k
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.6 years ago by ▴ 60 • written 3.6 years ago by ▴ 20
2
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3
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1.6k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.9 years ago by ▴ 160 • written 3.9 years ago by • 0
3
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2
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2.8k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.9 years ago camerond • 0
0
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7
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2.6k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.9 years ago • updated 3.8 years ago bge • 0
1
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3
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2.2k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.9 years ago by ★ 28k • written 4.0 years ago by ▴ 10
4
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5
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2.9k
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 660
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2
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1.5k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.0 years ago achaillon • 0
1
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3
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1.3k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.0 years ago by ▴ 70 • written 4.0 years ago by • 0
2
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3
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1.9k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.0 years ago achaillon • 0
0
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2
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1.7k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.0 years ago jirkanov • 0
2
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2
replies
2.5k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.0 years ago lirongrossmann ▴ 50
0
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1
reply
1.0k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 50
2
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7
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3.3k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 3.1 years ago by ★ 28k • written 4.1 years ago by ▴ 40
50 results • Page 1 of 1
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Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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