Showing : singlecellexperiment • reset
0
votes
0
replies
91
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
8 weeks ago Ibrahim • 0
0
votes
0
replies
150
views
News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
10 weeks ago info ▴ 10
2
votes
2
replies
409
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 3 months ago by ▴ 10
1
vote
1
reply
723
views
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
votes
1
reply
321
views
T cell subtype annotation
SingleCellExperiment
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
1
reply
1.2k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 5 months ago by • 0 • written 6 months ago by • 0
0
votes
0
replies
523
views
Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
6 months ago Stefano Mangiola ▴ 20
0
votes
4
replies
625
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
4
votes
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
4
votes
6
replies
1.0k
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
11 months ago Dario Strbenac ★ 1.5k
0
votes
0
replies
348
views
rpk per cell saved in SCE object.
SingleCellExperiment
11 months ago JalapenoCornbread • 0
1
vote
2
replies
1.3k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
12 months ago elgomez • 0
0
votes
7
replies
2.0k
views
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
votes
1
reply
773
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 14 months ago by • 0
2
votes
5
replies
1.3k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
16 months ago duez.tolga • 0
0
votes
2
replies
1.5k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
18 months ago Matvii Mykhailichenko • 0
0
votes
2
replies
1.3k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
18 months ago Lluís Revilla Sancho ▴ 760
1
vote
3
replies
2.9k
views
Remove certain highly expressing cells from a SCE
SingleCellExperiment
20 months ago • updated 19 months ago mollyab12 • 0
0
votes
1
reply
1.5k
views
Rename colData column
SingleCellExperiment colData rename
updated 22 months ago by ▴ 780 • written 22 months ago by ▴ 10
2
votes
3
replies
2.0k
views
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
votes
3
replies
2.1k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.3 years ago • updated 2.2 years ago merv ▴ 140
2
votes
2
replies
1.0k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.3 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
2.3 years ago Romina • 0
1
vote
1
reply
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
votes
1
reply
3.4k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.3 years ago merv ▴ 140
0
votes
0
replies
1.4k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.3 years ago merv ▴ 140
4
votes
3
replies
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
0
votes
1
reply
1.2k
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 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
2
votes
5
replies
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
votes
1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.7 years ago by ▴ 780 • written 2.7 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
2.8 years ago msn ▴ 10
0
votes
1
reply
876
views
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
votes
2
replies
1.4k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.0 years ago by ★ 4.6k • written 3.0 years ago by ▴ 40
0
votes
0
replies
781
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.1 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
3.1 years ago Fatima • 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.2 years ago • updated 3.1 years ago enricoferrero ▴ 660
0
votes
1
reply
3.2k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by • 0
2
votes
5
replies
5.7k
views
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
votes
3
replies
1.6k
views
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
votes
2
replies
2.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.9 years ago camerond • 0
0
votes
7
replies
2.6k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.9 years ago • updated 3.8 years ago bge • 0
1
vote
3
replies
2.2k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.9 years ago by ★ 28k • written 4.0 years ago by ▴ 10
4
votes
5
replies
2.9k
views
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
0
votes
2
replies
1.5k
views
from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.0 years ago achaillon • 0
1
vote
3
replies
1.3k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.0 years ago by ▴ 70 • written 4.0 years ago by • 0
2
votes
3
replies
1.9k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.0 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
4.0 years ago jirkanov • 0
2
votes
2
replies
2.5k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.0 years ago lirongrossmann ▴ 50
0
votes
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
votes
7
replies
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
Recent ...
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…
Votes
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
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
The city by the bay, 39 minutes ago
WEHI, Melbourne, Australia, 47 minutes ago
United Kingdom, 1 hour ago
United States, 2 hours ago
UPF, Barcelona, Spain, 4 hours ago
Traffic: 444 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