Showing : batchelor • reset
3
votes
6
replies
2.1k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 3.0 years ago by ★ 28k • written 3.0 years ago by • 0
3
votes
3
replies
1.8k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 2.8 years ago by ★ 28k • written 2.8 years ago by ★ 2.9k
2
votes
3
replies
1.3k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 2.8 years ago by ★ 28k • written 2.8 years ago by • 0
2
votes
2
replies
1.0k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 10 months ago by ▴ 40 • written 3.4 years ago by • 0
0
votes
2
replies
955
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
2.5 years ago jirkanov • 0
0
votes
2
replies
926
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 2.4 years ago by ▴ 50 • written 2.4 years ago by ▴ 70
2
votes
7
replies
915
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
11 months ago pcantalupo • 0
0
votes
4
replies
902
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 9 months ago by ★ 28k • written 10 months ago by ▴ 40
1
vote
2
replies
870
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
3
votes
3
replies
860
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 10
2
votes
6
replies
740
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 2.9 years ago by ★ 28k • written 2.9 years ago by • 0
1
vote
1
reply
705
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 2.5 years ago by ★ 28k • written 2.6 years ago by • 0
2
votes
1
reply
676
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 3.1 years ago by ★ 28k • written 3.8 years ago by ▴ 20
2
votes
1
reply
676
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ★ 2.9k
1
vote
5
replies
594
views
batch effect
TargetScoreData batchelor
written 10 months ago by ▴ 10
2
votes
2
replies
579
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
20 months ago p.joshi ▴ 40
4
votes
2
replies
548
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
10 months ago • updated 9 months ago Guandong Shang ▴ 40
0
votes
4
replies
541
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 3 months ago by • 0 • written 3.2 years ago by • 0
18 results • Page 1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind by Chris • 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind by Chris • 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting by phelankj • 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting by James W. MacDonald 63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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