RECODE documentation
Resolution of the curse of dimensionality (RECODE) is a noise reduction method for single-cell sequencing data. github
Y. Imoto. Comprehensive Noise Reduction in Single-Cell Data with the RECODE Platform, 2024, bioRxiv.
The license gives permission for personal, academic, or educational use. Any commercial use is strictly prohibited. Please contact imoto.yusuke.4e<at>kyoto-u.ac.jp for licensing terms for any commercial use.
Installation
The python package of RECODE supports PyPI install.
$ pip install screcode
You can also install the development version of lingam package from GitHub:
$ pip install git+https://github.com/yusuke-imoto-lab/RECODE.git
If the installation fails, try installing again by appending #subdirectory=python or #subdirectory=python at the end.
To use RECODE, import screcode.
import screcode
The R package is available here.
Contents:
- Tutorials
- Transcriptome (scRNA-seq data)
- Transcriptome (scRNA-seq data) + HVG selection
- Chromatin accessibility (scATAC-seq data)
- Multiome (scRNA-seq + scATAC-seq data)
- Spatial transcriptome (Stereo-seq)
- Spatial transcriptome (VisiumHD)
- Spatial transcriptome (Xenium)
- Spatial transcriptome (Xenium Prime)
- Integration (iRECODE)
- API Reference