Showing : SingleCellExperiment • reset
0
votes
1
reply
314
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 27 days ago by ★ 4.0k • written 3 months ago by • 0
1
vote
2
replies
444
views
Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 5 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
0
votes
0
replies
156
views
News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
3 months ago Ludwig Geistlinger ▴ 70
3
votes
9
replies
4.6k
views
Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 6 weeks ago by • 0 • written 5 months ago by ▴ 10
4
votes
17
replies
5.8k
views
How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 6 months ago by ★ 5.0k • written 7 months ago by ▴ 10
1
vote
3
replies
1.2k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
6 months ago Konstantinos Yeles ▴ 90
3
votes
2
replies
801
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 9 months ago by ▴ 40 • written 11 months ago by • 0
0
votes
0
replies
378
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
14 months ago Ibrahim • 0
0
votes
0
replies
577
views
News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
14 months ago info ▴ 10
2
votes
2
replies
867
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 15 months ago by ▴ 10
2
votes
1
reply
2.2k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 16 months ago by ★ 29k • written 16 months ago by • 0
0
votes
1
reply
699
views
T cell subtype annotation
SingleCellExperiment
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
1
reply
3.5k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 17 months ago by • 0 • written 18 months ago by • 0
0
votes
0
replies
999
views
Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
18 months ago Stefano Mangiola ▴ 40
0
votes
4
replies
1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
18 months ago vohara4 • 0
4
votes
1
reply
1.9k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 23 months ago by 68k • written 23 months ago by ▴ 20
4
votes
6
replies
1.6k
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
23 months ago Dario Strbenac ★ 1.6k
0
votes
0
replies
543
views
rpk per cell saved in SCE object.
SingleCellExperiment
23 months ago JalapenoCornbread • 0
1
vote
2
replies
1.8k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
2.0 years ago elgomez • 0
0
votes
10
replies
3.8k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 2.0 years ago by • 0
0
votes
1
reply
1.1k
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.2 years ago by • 0
2
votes
5
replies
1.8k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.4 years ago • updated 2.3 years ago duez.tolga • 0
0
votes
2
replies
2.0k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.5 years ago Matvii Mykhailichenko • 0
0
votes
2
replies
1.9k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.5 years ago Lluís Revilla Sancho ▴ 760
1
vote
3
replies
3.9k
views
Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.6 years ago mollyab12 • 0
0
votes
1
reply
2.1k
views
Rename colData column
SingleCellExperiment colData rename
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by ▴ 10
2
votes
3
replies
2.5k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.9 years ago by ▴ 40 • written 6.9 years ago by ▴ 10
4
votes
3
replies
2.9k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.3 years ago • updated 3.2 years ago merv ▴ 150
2
votes
4
replies
2.1k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 20
2
votes
4
replies
1.7k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.3 years ago Romina • 0
1
vote
1
reply
2.4k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 3.3 years ago by ▴ 760 • written 3.3 years ago by ▴ 150
5
votes
1
reply
4.0k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
3.3 years ago merv ▴ 150
0
votes
0
replies
1.8k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
3.3 years ago merv ▴ 150
4
votes
3
replies
2.7k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 10
0
votes
1
reply
1.6k
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 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
2
votes
5
replies
6.5k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.8 years ago by • 0 • written 3.6 years ago by ▴ 10
2
votes
1
reply
1.9k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
vote
2
replies
1.6k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.8 years ago msn ▴ 10
0
votes
1
reply
1.1k
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
2
votes
2
replies
1.8k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by ▴ 40
0
votes
0
replies
1.0k
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
4.0 years ago Núria • 0
1
vote
2
replies
1.4k
views
Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
4.1 years ago Fatima • 0
3
votes
3
replies
2.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.1 years ago enricoferrero ▴ 680
0
votes
1
reply
3.9k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
2
votes
5
replies
7.0k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.6 years ago by ▴ 60 • written 4.6 years ago by ▴ 20
2
votes
3
replies
2.0k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.9 years ago by ▴ 160 • written 4.9 years ago by • 0
3
votes
2
replies
3.5k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.9 years ago camerond • 0
0
votes
7
replies
3.2k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.9 years ago • updated 4.8 years ago bge • 0
1
vote
3
replies
2.6k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 10
4
votes
5
replies
3.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 680
93 results • Page 1 of 2
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Michael Love 43k
Popular Question to Luca • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to James W. MacDonald 68k
Locations • All
United States, 6 minutes ago
Singapore, 43 minutes ago
Italy, 50 minutes ago
The city by the bay, 1 hour ago
Germany, 3 hours ago
Traffic: 1170 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