Showing : batchelor • reset
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6
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fastMNN reproducibility across machines when using Docker
batchelor
10 months ago nils.eling • 0
4
votes
2
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1.1k
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how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
20 months ago Guandong Shang ▴ 40
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4
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2.0k
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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
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5
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1.2k
views
batch effect
TargetScoreData batchelor
written 20 months ago by ▴ 10
2
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7
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1.4k
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batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
22 months ago pcantalupo ▴ 10
2
votes
2
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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
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2
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1.4k
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Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 3.3 years ago by ▴ 50 • written 3.3 years ago by ▴ 70
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2
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1.4k
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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
1
vote
1
reply
993
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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
2
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3
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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
3
votes
3
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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
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
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
6
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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
1.0k
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
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
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
0
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4
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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
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
19 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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