Reference mapping for single-cell genomics

R package for the joint analysis of multiple single-cell RNA-seq datasets

Testing differences in cell type proportions from single-cell data.

Harmony framework for connecting scRNA-seq data from discrete time points

Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)

single cell foundation model for Gene network inference and more

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Clone of the Bioconductor repository for the batchelor package.

MAAPster is a comprehensive tool to perform transcriptome analysis of human or mouse Affymetrix gene expression data

Methylation array preprocessing.

Detecting and dissecting anomalous anatomic regions in spatial transcriptomics with STANDS

Towards Backwards-Compatible Data with Confounded Domain Adaptation (TMLR, 2024)

A similarity-assisted variational autoencoder (saVAE) is a new method that adopts similarity information in the framework of the VAE.

A comparison of data integration methods for single-cell RNA sequencing of cancer samples

M2ASDA

Batman: Batch effect correction via minimum weight MAtchiNg

A Python tool for performing downstream analysis on Single-Cell RNA-seq datasets

Comparison of batch correction methods for scRNA-seq data - basically a clone of BatchBench

An R tool to detect and correct batch-effects in gene-expression data (Microarray and bulk-RNAseq))

An R package for the alignment and scaling of LC-MS metabolomics data