Showing : batchelor • reset
0
votes
2
replies
1.1k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
13 months ago José • 0
2
votes
2
replies
859
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 15 months ago by ▴ 10
0
votes
6
replies
1.5k
views
fastMNN reproducibility across machines when using Docker
batchelor
2.5 years ago nils.eling ▴ 10
4
votes
2
replies
1.9k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.3 years ago Guandong Shang ▴ 40
0
votes
4
replies
3.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.3 years ago by ★ 29k • written 3.4 years ago by ▴ 40
1
vote
5
replies
1.9k
views
batch effect
TargetScoreData batchelor
written 3.3 years ago by ▴ 10
2
votes
7
replies
2.3k
views
batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
3.5 years ago • updated 3.4 years ago pcantalupo ▴ 10
2
votes
2
replies
1.7k
views
Does MNN removes same average batch vector from all cells or each cell has it's own correction vector?
fastmnn batchelor BatchEffect
4.2 years ago p.joshi ▴ 40
0
votes
2
replies
2.3k
views
Error coercing LowRankMatrix to dgCMatrix
BiocSingular zellkonverter batchelor
updated 4.9 years ago by ▴ 50 • written 4.9 years ago by ▴ 70
0
votes
2
replies
2.1k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
5.0 years ago jirkanov • 0
1
vote
1
reply
1.6k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 5.1 years ago by ★ 29k • written 5.1 years ago by • 0
2
votes
3
replies
2.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
3
votes
3
replies
3.6k
views
Cell cycle regression for scRNA-seq data
OSCA batchelor cell cycle regression
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ★ 5.0k
2
votes
6
replies
1.9k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.4 years ago by ★ 29k • written 5.5 years ago by • 0
3
votes
1
reply
1.8k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ★ 5.0k
3
votes
6
replies
4.2k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 5.5 years ago by ★ 29k • written 5.5 years ago by • 0
2
votes
1
reply
1.6k
views
batchelor batch correction correction runs into errors
batchelor batch-correction mnncorrect fastmnn rna-seq
updated 5.7 years ago by ★ 29k • written 6.3 years ago by ▴ 20
3
votes
3
replies
2.1k
views
MNN batch correction of pre-computed PCA
single cell batchelor
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 10
1
vote
2
replies
2.1k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN CITE-seq ADT-seq batchelor REAP-seq
updated 5.7 years ago by ★ 29k • written 5.7 years ago by • 0
0
votes
5
replies
3.0k
views
How to perform batch correction on scRNA-seq with confounding plate effects?
batchelor
updated 7 months ago by • 0 • written 5.7 years ago by • 0
2
votes
2
replies
2.7k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 3.3 years ago by ▴ 40 • written 5.9 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Locations • All
WEHI, Melbourne, Australia, 3 hours ago
The city by the bay, 4 hours ago
Seattle, WA, United States, 4 hours ago
United States, 4 hours ago
United States, 5 hours ago
Traffic: 922 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