Showing : batchelor • reset
0
votes
2
replies
588
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
3 months ago José • 0
2
votes
2
replies
474
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 4 months ago by ▴ 10
0
votes
6
replies
1.1k
views
fastMNN reproducibility across machines when using Docker
batchelor
19 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
2.5 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.5 years ago by ★ 28k • written 2.5 years ago by ▴ 40
1
vote
5
replies
1.5k
views
batch effect
TargetScoreData batchelor
written 2.5 years ago by ▴ 10
2
votes
7
replies
1.9k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
2.6 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
3.3 years ago p.joshi ▴ 40
0
votes
2
replies
1.8k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 4.0 years ago by ▴ 50 • written 4.0 years ago by ▴ 70
0
votes
2
replies
1.7k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.1 years ago jirkanov • 0
1
vote
1
reply
1.3k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 4.2 years ago by ★ 28k • written 4.2 years ago by • 0
2
votes
3
replies
2.3k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
3
votes
3
replies
3.0k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 4.4 years ago by ★ 28k • written 4.5 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 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
3
votes
1
reply
1.4k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ★ 4.6k
3
votes
6
replies
3.5k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 4.7 years ago by ★ 28k • written 4.7 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 4.8 years ago by ★ 28k • written 5.4 years ago by ▴ 20
3
votes
3
replies
1.7k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 10
1
vote
2
replies
1.7k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
votes
4
replies
1.5k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 23 months ago by • 0 • written 4.9 years ago by • 0
2
votes
2
replies
2.1k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 2.5 years ago by ▴ 40 • written 5.0 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
Votes
Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Awards • All
Popular Question to Maria Doyle ▴ 100
Popular Question to Robert Ivanek ▴ 750
Popular Question to shepherl 4.1k
Popular Question to Gordon Smyth 52k
Popular Question to Koen Van den Berge ▴ 180
Locations • All
WEHI, Melbourne, Australia, 6 minutes ago
United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
United States, 2 hours ago
Traffic: 736 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6