singlecell-batches's repositories
cookiecutter-pypackage-from-czb
Cookiecutter template for a Python package. See https://github.com/audreyr/cookiecutter.
vamf
Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing
data
Repository organizing the data behind the singlecell batch effect correction comparison project
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."
mutual-nearest-neighbors
Algorithm to correct batch effects for batches with different cell population
singularity
How to use Singularity containers for running single cell batch effect correction algorithms
getting-started
How to get started with the single cell batches comparison
manuscript
Landing page for manuscript comparing single-cell batch effect correction algorithms
algorithm-template
boilerplate for reproducible and transparent science
scPLS
method is based on partial least squares and models control and target genes jointly to better infer and control for confounding effects
deprecated-algorithm-template
Template for adding an algorithm for analysis with single cell batch effects
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
biscuit
One smart cookie of an algorithm. Infers both batch effects and clusters at the same time.
deprecated-manuscript
Paper for comparison of batch effect correction algorithms in single-cell RNA-seq