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batchelor
•
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0
votes
6
replies
744
views
fastMNN reproducibility across machines when using Docker
batchelor
11 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
22 months ago
Guandong Shang
▴ 40
0
votes
4
replies
2.1k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 22 months ago by
Aaron Lun
★ 28k • written 22 months ago by
Guandong Shang
▴ 40
1
vote
5
replies
1.2k
views
batch effect
TargetScoreData
batchelor
written 22 months ago by
Syed Zaheer
▴ 10
2
votes
7
replies
1.5k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
23 months ago
pcantalupo
▴ 10
2
votes
2
replies
994
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn
batchelor
BatchEffect
2.7 years ago
p.joshi
▴ 40
0
votes
2
replies
1.4k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular
zellkonverter
batchelor
updated 3.4 years ago by
luke.zappia
▴ 50 • written 3.4 years ago by
jma1991
▴ 70
0
votes
2
replies
1.5k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
3.5 years ago
jirkanov
• 0
1
vote
1
reply
1.0k
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Adrien
• 0
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
Angelos Armen
• 0
3
votes
3
replies
2.5k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
ATpoint
★ 4.2k
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
Angelos Armen
• 0
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
ATpoint
★ 4.2k
3
votes
6
replies
3.0k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
heir_of_isildur88
• 0
2
votes
1
reply
1.0k
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
rmf
▴ 20
3
votes
3
replies
1.3k
views
MNN batch correction of pre-computed PCA
single cell
batchelor
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
tahvdbrand
▴ 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 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
sorjuelal
• 0
0
votes
4
replies
1.1k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 15 months ago by
Ivo Kwee
• 0 • written 4.2 years ago by
jashmore
• 0
2
votes
2
replies
1.6k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 22 months ago by
Guandong Shang
▴ 40 • written 4.4 years ago by
heir_of_isildur88
• 0
19 results • Page
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Comment: How to compare subset of samples from VCF files
by
Gordon Smyth
50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files
by
Marco
• 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database
by
James W. MacDonald
66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database
by
luigi.faino
• 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database
by
James W. MacDonald
66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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