Showing : batchelor • reset
0
votes
6
replies
394
views
fastMNN reproducibility across machines when using Docker
batchelor
3 months ago nils.eling • 0
4
votes
2
replies
734
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
13 months ago Guandong Shang ▴ 40
0
votes
4
replies
1.4k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 13 months ago by ★ 28k • written 14 months ago by ▴ 40
1
vote
5
replies
799
views
batch effect
TargetScoreData batchelor
written 13 months ago by ▴ 10
2
votes
7
replies
1.1k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
15 months ago pcantalupo • 0
2
votes
2
replies
702
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
24 months ago p.joshi ▴ 40
0
votes
2
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1.1k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 2.7 years ago by ▴ 50 • written 2.7 years ago by ▴ 70
0
votes
2
replies
1.1k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
2.8 years ago jirkanov • 0
1
vote
1
reply
796
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 2.9 years ago by ★ 28k • written 2.9 years ago by • 0
2
votes
3
replies
1.4k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 3.1 years ago by ★ 28k • written 3.1 years ago by • 0
3
votes
3
replies
2.0k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ★ 3.4k
2
votes
6
replies
904
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.2 years ago by ★ 28k • written 3.3 years ago by • 0
2
votes
1
reply
846
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ★ 3.4k
3
votes
6
replies
2.3k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 0
2
votes
1
reply
781
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 3.5 years ago by ★ 28k • written 4.1 years ago by ▴ 20
3
votes
3
replies
1.0k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 10
1
vote
2
replies
1.0k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
votes
4
replies
705
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 7 months ago by • 0 • written 3.5 years ago by • 0
2
votes
2
replies
1.2k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 13 months ago by ▴ 40 • written 3.7 years ago by • 0
19 results • Page 1 of 1
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Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by Mike Smith ★ 6.1k
I'll echo James' suggestion to use the GRCh37 mirror. Most mirrors only have a guaranteed lifetime of 5 years from Ensembl, although it se…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by James W. MacDonald 63k
I should also point out that you can find this out by yourself by going to [ensembl][1], clicking on the Biomart link, and then scrolling t…
Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by James W. MacDonald 63k
It's my understanding that the archived Biomart data are not complete, which is likely why you cannot get sequences. But you apparently jus…
Comment: ComBat_seq function in sva package does not return a matrix by Federico ▴ 10
Thanks for your help, problem solved :)
Answer: ComBat_seq function in sva package does not return a matrix by ATpoint ★ 3.4k
That happens if your `x` is a data.frame rather than a matrix. It is listed under the Q&A section in https://github.com/zhangyuqing/ComBat-…
Votes
ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
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