piaso-tools 1.0.1

Precise Integrative Analysis of Single-cell Omics.

PIASO

Precise Integrative Analysis of Single-cell Omics

Documentation

PIASO documentation

Current available functionalities

1. perform dimensionality reduction with GDR
2. integration of scRNA-seq datasets with GDR
3. integration of scRNA-seq data and MERFISH/Xenium data with GDR
4. normalization of scRNA-seq data with INFOG
5. selection of highly-variable genes in scRNAseq data with INFOG
6. a novel gene set scoring method
7. run clustering on selected cluster(s)
8. side-by-side cell embedding plots, e.g., split by Conditions
9. stacked violin plots for multiple features, including genes and cell metrics

Coming functionalities

1. preprocessing of scATAC-seq datasets
2. integration of scRNA-seq and scATAC-seq datasets (not relying on gene activities)
3. inference of cell type-specific gene regulatory networks
4. and others

Installation

You could simply install PIASO via pip in your conda environment:

pip install piaso-tools

For the development version in GitHub, you could install via:

pip install git+https://github.com/genecell/PIASO.git

Citation

If PIASO is useful for your research, please consider citing Wu et al., Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes, bioRxiv (2024).

Contact

Min Dai [e-mail]