Showing : batchelor • reset
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2
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
10 months ago José • 0
2
votes
2
replies
736
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 12 months ago by ▴ 10
0
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6
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1.4k
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fastMNN reproducibility across machines when using Docker
batchelor
2.2 years ago nils.eling ▴ 10
4
votes
2
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1.8k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.1 years ago Guandong Shang ▴ 40
0
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4
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2.9k
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how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.1 years ago by ★ 29k • written 3.1 years ago by ▴ 40
1
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5
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1.7k
views
batch effect
TargetScoreData batchelor
written 3.1 years ago by ▴ 10
2
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7
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2.1k
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batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
3.2 years ago pcantalupo ▴ 10
2
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2
replies
1.6k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
3.9 years ago p.joshi ▴ 40
0
votes
2
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2.2k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 4.6 years ago by ▴ 50 • written 4.6 years ago by ▴ 70
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2
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2.0k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.7 years ago jirkanov • 0
1
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1
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1.5k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 4.8 years ago by ★ 29k • written 4.8 years ago by • 0
2
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3
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2.6k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 5.0 years ago by ★ 29k • written 5.0 years ago by • 0
3
votes
3
replies
3.5k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ★ 4.9k
2
votes
6
replies
1.8k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.2 years ago by ★ 29k • written 5.2 years ago by • 0
3
votes
1
reply
1.7k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ★ 4.9k
3
votes
6
replies
4.0k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
2
votes
1
reply
1.5k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 5.4 years ago by ★ 29k • written 6.0 years ago by ▴ 20
3
votes
3
replies
2.0k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 10
1
vote
2
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2.0k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
0
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5
replies
2.8k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 4 months ago by • 0 • written 5.5 years ago by • 0
2
votes
2
replies
2.5k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 3.1 years ago by ▴ 40 • written 5.6 years ago by • 0
21 results • Page 1 of 1
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Comment: Biological Pathway Database by peterparkerrbu • 0
Having the pathways available in PowerPoint format is a huge plus, as it makes them easy to use for presentations and teaching. The ability…
Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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