Showing : singleCellExperiment • reset
0
votes
1
reply
296
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
4
votes
6
replies
563
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
3 months ago Dario Strbenac ★ 1.5k
0
votes
0
replies
156
views
rpk per cell saved in SCE object.
SingleCellExperiment
3 months ago JalapenoCornbread • 0
0
votes
3
replies
493
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 4 months ago by • 0 • written 4 months ago by • 0
1
vote
2
replies
935
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
4 months ago elgomez • 0
0
votes
1
reply
502
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 6 months ago by • 0
1
vote
3
replies
1.8k
views
Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
written 5.1 years ago by ▴ 350
1
vote
5
replies
848
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
votes
2
replies
899
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
0
votes
2
replies
821
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
10 months ago Lluís Revilla Sancho ▴ 730
1
vote
3
replies
2.0k
views
Remove certain highly expressing cells from a SCE
SingleCellExperiment
12 months ago mollyab12 • 0
2
votes
5
replies
4.1k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 14 months ago by • 0 • written 2.0 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Rename colData column
SingleCellExperiment colData rename
updated 14 months ago by ▴ 780 • written 14 months 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 15 months ago by ▴ 10 • written 5.3 years ago by ▴ 10
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
788
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
19 months ago k1m ▴ 20
2
votes
4
replies
913
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago • updated 19 months ago Romina • 0
1
vote
1
reply
1.1k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 20 months ago by ▴ 740 • written 20 months ago by ▴ 120
4
votes
1
reply
2.2k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
20 months ago merv ▴ 120
0
votes
0
replies
1.0k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
20 months ago merv ▴ 120
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
0
votes
1
reply
972
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 22 months ago by ★ 4.1k • written 22 months ago by • 0
2
votes
1
reply
1.1k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
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
1
vote
2
replies
924
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.2 years ago msn ▴ 10
0
votes
1
reply
718
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
2
votes
2
replies
1.2k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 40
0
votes
0
replies
633
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.4 years ago Núria • 0
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
1
vote
2
replies
841
views
Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
2.5 years ago Fatima • 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
0
votes
1
reply
2.6k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by • 0
2
votes
5
replies
4.9k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 2.9 years ago by ▴ 60 • written 3.0 years ago by ▴ 20
0
votes
7
replies
2.1k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.3 years ago • updated 3.2 years ago bge • 0
3
votes
2
replies
2.2k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
2
votes
3
replies
1.3k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.2 years ago by ▴ 160 • written 3.2 years ago by • 0
2
votes
4
replies
2.3k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.3 years ago by • 0 • written 4.1 years ago by • 0
1
vote
3
replies
1.9k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 10
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
0
votes
2
replies
1.2k
views
from phenograph output to singlecellexperiment object with metadata
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
1
vote
3
replies
1.5k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.4 years ago achaillon • 0
0
votes
2
replies
1.4k
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
2
replies
2.0k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.4 years ago lirongrossmann ▴ 40
0
votes
1
reply
831
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
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
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
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
0
votes
0
replies
747
views
Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.7 years ago lirongrossmann ▴ 80
0
votes
3
replies
2.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
Switzerland, 2 minutes ago
Germany, 9 minutes ago
United Kingdom, 11 minutes ago
France, 13 minutes ago
Sweden, 17 minutes ago
Traffic: 766 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