Showing : batchelor • reset
0
votes
2
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485
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
8 weeks ago José • 0
2
votes
2
replies
408
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 3 months ago by ▴ 10
0
votes
6
replies
1.0k
views
fastMNN reproducibility across machines when using Docker
batchelor
18 months ago nils.eling ▴ 10
4
votes
2
replies
1.5k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.4 years ago Guandong Shang ▴ 40
0
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4
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2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 40
1
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5
replies
1.5k
views
batch effect
TargetScoreData batchelor
written 2.4 years ago by ▴ 10
2
votes
7
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1.8k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
2.5 years ago pcantalupo ▴ 10
2
votes
2
replies
1.3k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
3.2 years ago p.joshi ▴ 40
0
votes
2
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1.8k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 3.9 years ago by ▴ 50 • written 3.9 years ago by ▴ 70
0
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2
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1.7k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.0 years ago jirkanov • 0
1
vote
1
reply
1.2k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
2
votes
3
replies
2.2k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
3
votes
3
replies
2.9k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ★ 4.6k
2
votes
6
replies
1.4k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
3
votes
1
reply
1.4k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ★ 4.6k
3
votes
6
replies
3.4k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
2
votes
1
reply
1.3k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 4.7 years ago by ★ 28k • written 5.3 years ago by ▴ 20
3
votes
3
replies
1.7k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 10
1
vote
2
replies
1.6k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
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4
replies
1.4k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 22 months ago by • 0 • written 4.8 years ago by • 0
2
votes
2
replies
2.0k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 2.4 years ago by ▴ 40 • written 4.9 years ago by • 0
21 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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