singlecell-batches Goto Github PK

algorithm-template

boilerplate for reproducible and transparent science

awesome-algorithms-list

biscuit

One smart cookie of an algorithm. Infers both batch effects and clusters at the same time.

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.

data

Repository organizing the data behind the singlecell batch effect correction comparison project

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)

manuscript

Landing page for manuscript comparing single-cell batch effect correction algorithms

mutual-nearest-neighbors

Algorithm to correct batch effects for batches with different cell population

scpls

method is based on partial least squares and models control and target genes jointly to better infer and control for confounding effects

singularity

How to use Singularity containers for running single cell batch effect correction algorithms

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