Showing : batchelor • reset
0
votes
6
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674
views
fastMNN reproducibility across machines when using Docker
batchelor
9 months ago nils.eling • 0
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
20 months ago Guandong Shang ▴ 40
0
votes
4
replies
2.0k
views
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 20 months ago by ▴ 40
1
vote
5
replies
1.1k
views
batch effect
TargetScoreData batchelor
written 20 months ago by ▴ 10
2
votes
7
replies
1.4k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
22 months ago • updated 21 months ago pcantalupo ▴ 10
2
votes
2
replies
945
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
0
votes
2
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1.4k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 3.2 years ago by ▴ 50 • written 3.2 years ago by ▴ 70
0
votes
2
replies
1.4k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.4 years ago • updated 3.3 years ago jirkanov • 0
1
vote
1
reply
984
views
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
votes
3
replies
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
replies
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 3.8 years ago by ★ 28k • written 3.8 years ago by ★ 4.0k
3
votes
6
replies
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
993
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
votes
4
replies
1.0k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 13 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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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) …
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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