RECODE documentation

Resolution of the curse of dimensionality (RECODE) is a noise reduction method for single-cell sequencing data. github

Y. Imoto, T. Nakamura, et al. Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis, 2022, Life Science Alliance.

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)
  • 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
  • RECODE

Indices and tables

• Index

• Module Index

• Search Page