Showing : batchelor • reset
0
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2
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
13 months ago José • 0
2
votes
2
replies
845
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 14 months ago by ▴ 10
0
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6
replies
1.5k
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fastMNN reproducibility across machines when using Docker
batchelor
2.4 years ago nils.eling ▴ 10
4
votes
2
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1.9k
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how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.3 years ago Guandong Shang ▴ 40
0
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4
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3.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.3 years ago by ★ 29k • written 3.3 years ago by ▴ 40
1
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5
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1.9k
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batch effect
TargetScoreData batchelor
written 3.3 years ago by ▴ 10
2
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7
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2.3k
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batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
3.5 years ago • updated 3.4 years ago pcantalupo ▴ 10
2
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2
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1.7k
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Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
4.2 years ago p.joshi ▴ 40
0
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2
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2.3k
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Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 4.9 years ago by ▴ 50 • written 4.9 years ago by ▴ 70
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2
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2.1k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
5.0 years ago jirkanov • 0
1
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1
reply
1.6k
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Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 5.0 years ago by ★ 29k • written 5.0 years ago by • 0
2
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3
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2.7k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
3
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3
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3.6k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ★ 5.0k
2
votes
6
replies
1.9k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
3
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1
reply
1.8k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ★ 5.0k
3
votes
6
replies
4.2k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 5.5 years ago by ★ 29k • written 5.5 years ago by • 0
2
votes
1
reply
1.6k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 5.6 years ago by ★ 29k • written 6.3 years ago by ▴ 20
3
votes
3
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2.0k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 5.6 years ago by ★ 29k • written 5.6 years ago by ▴ 10
1
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2
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2.1k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 5.7 years ago by ★ 29k • written 5.7 years ago by • 0
0
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5
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3.0k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 7 months ago by • 0 • written 5.7 years ago by • 0
2
votes
2
replies
2.6k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 3.3 years ago by ▴ 40 • written 5.9 years ago by • 0
21 results • Page 1 of 1
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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