Showing : batchelor • reset
2
votes
6
replies
1.1k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
2
votes
2
replies
1.5k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 20 months ago by ▴ 40 • written 4.3 years ago by • 0
0
votes
4
replies
1.0k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 14 months ago by • 0 • written 4.1 years ago by • 0
1
vote
2
replies
1.3k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
3
votes
3
replies
1.3k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 10
3
votes
6
replies
2.9k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ★ 4.0k
3
votes
3
replies
2.4k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ★ 4.0k
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
1
vote
1
reply
996
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 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
0
votes
2
replies
1.4k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 3.3 years ago by ▴ 50 • written 3.3 years ago by ▴ 70
2
votes
7
replies
1.4k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
22 months ago pcantalupo ▴ 10
2
votes
1
reply
1.0k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 4.0 years ago by ★ 28k • written 4.7 years ago by ▴ 20
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
20 months ago Guandong Shang ▴ 40
2
votes
2
replies
956
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
2.6 years ago p.joshi ▴ 40
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 20 months ago by ★ 28k • written 21 months ago by ▴ 40
1
vote
5
replies
1.2k
views
batch effect
TargetScoreData batchelor
written 20 months ago by ▴ 10
0
votes
6
replies
691
views
fastMNN reproducibility across machines when using Docker
batchelor
10 months ago nils.eling • 0
19 results • Page 1 of 1
Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Hi, Yes, I've tried this, but I am not sure if it is possible to assign `bquote` values to the names of a vector. In particular, if I use…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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