Pinned Repositories
ccRemover
The algorithm identifies and removes cell cycle effects from single cell mRNAseq data
combat
removes batch effects, good for small sample sizes, mean-centric
cookiecutter-pypackage-from-czb
Cookiecutter template for a Python package. See https://github.com/audreyr/cookiecutter.
deprecated-algorithm-template
Template for adding an algorithm for analysis with single cell batch effects
deprecated-manuscript
Paper for comparison of batch effect correction algorithms in single-cell RNA-seq
distribution-matching-residual-networks
"We propose a novel deep learning approach for removing systematic batch effects. Our method is based on a residual neural network, trained to minimize the Maximum Mean Discrepancy between the multivariate distributions of two replicates, measured in different batches."
getting-started
How to get started with the single cell batches comparison
limma
removeBatchEffect function (remove batch effect from expression data)
this-is-how-we-batch-it
Algorithm for removing batch effects in single-cell RNA-seq that leaves only the batches that are having the most fun
vamf
Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing
singlecell-batches's Repositories
singlecell-batches/getting-started
How to get started with the single cell batches comparison
singlecell-batches/ccRemover
The algorithm identifies and removes cell cycle effects from single cell mRNAseq data
singlecell-batches/combat
removes batch effects, good for small sample sizes, mean-centric
singlecell-batches/cookiecutter-pypackage-from-czb
Cookiecutter template for a Python package. See https://github.com/audreyr/cookiecutter.
singlecell-batches/deprecated-algorithm-template
Template for adding an algorithm for analysis with single cell batch effects
singlecell-batches/deprecated-manuscript
Paper for comparison of batch effect correction algorithms in single-cell RNA-seq
singlecell-batches/distribution-matching-residual-networks
"We propose a novel deep learning approach for removing systematic batch effects. Our method is based on a residual neural network, trained to minimize the Maximum Mean Discrepancy between the multivariate distributions of two replicates, measured in different batches."
singlecell-batches/limma
removeBatchEffect function (remove batch effect from expression data)
singlecell-batches/this-is-how-we-batch-it
Algorithm for removing batch effects in single-cell RNA-seq that leaves only the batches that are having the most fun
singlecell-batches/vamf
Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing
singlecell-batches/algorithm-template
boilerplate for reproducible and transparent science
singlecell-batches/awesome-algorithms-list
singlecell-batches/biscuit
One smart cookie of an algorithm. Infers both batch effects and clusters at the same time.
singlecell-batches/data
Repository organizing the data behind the singlecell batch effect correction comparison project
singlecell-batches/manuscript
Landing page for manuscript comparing single-cell batch effect correction algorithms
singlecell-batches/mutual-nearest-neighbors
Algorithm to correct batch effects for batches with different cell population
singlecell-batches/scPLS
method is based on partial least squares and models control and target genes jointly to better infer and control for confounding effects
singlecell-batches/singularity
How to use Singularity containers for running single cell batch effect correction algorithms