Showing : batchelor • reset
0
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2
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1.1k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
11 months ago José • 0
2
votes
2
replies
779
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 13 months ago by ▴ 10
0
votes
6
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1.4k
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fastMNN reproducibility across machines when using Docker
batchelor
2.3 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
3.2 years ago Guandong Shang ▴ 40
0
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4
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2.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 40
1
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5
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1.8k
views
batch effect
TargetScoreData batchelor
written 3.2 years ago by ▴ 10
2
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7
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2.2k
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batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
3.3 years ago pcantalupo ▴ 10
2
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2
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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
4.0 years ago p.joshi ▴ 40
0
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2
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2.2k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 4.7 years ago by ▴ 50 • written 4.7 years ago by ▴ 70
0
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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
4.8 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 4.9 years ago by ★ 29k • written 4.9 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 5.1 years ago by ★ 29k • written 5.1 years ago by • 0
3
votes
3
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3.5k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ★ 5.0k
2
votes
6
replies
1.8k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
3
votes
1
reply
1.7k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ★ 5.0k
3
votes
6
replies
4.1k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 5.4 years ago by ★ 29k • written 5.4 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 5.5 years ago by ★ 29k • written 6.1 years ago by ▴ 20
3
votes
3
replies
2.0k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ▴ 10
1
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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 5.5 years ago by ★ 29k • written 5.5 years ago by • 0
0
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5
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2.9k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 5 months ago by • 0 • written 5.6 years ago by • 0
2
votes
2
replies
2.5k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 3.2 years ago by ▴ 40 • written 5.7 years ago by • 0
21 results • Page 1 of 1
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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