Metadata-Version: 2.1
Name: xcltk
Version: 0.5.2
Summary: xcltk - Toolkit for XClone
Home-page: https://github.com/hxj5/xcltk
Author: Xianjie Huang
Author-email: xianjie5@connect.hku.hk
License: Apache-2.0
Description: # xcltk: Toolkit for XClone Preprocessing
        
        [![](https://img.shields.io/pypi/v/xcltk.svg)][pypi]
        [![](https://img.shields.io/github/license/hxj5/xcltk)][licence]
        
        
        [XClone][XClone repo] is a statistical method to detect allele- and 
        haplotype-specific copy number variations (CNVs) and reconstruct 
        tumour clonal substructure from scRNA-seq data, 
        by integrating the expression levels (read depth ratio; RDR signals) and 
        the allelic balance (B-allele frequency; BAF signals).
        It takes three matrices as input: the allele-specific *AD* and *DP* matrices
        (BAF signals) and the *total read depth* matrix (RDR signals).
        
        The [xcltk][xcltk repo] package implements a preprocessing pipeline to 
        generate the three matrices from SAM/BAM/CRAM files.
        It supports data from multiple single-cell sequencing platforms, including 
        droplet-based (e.g., 10x Genomics) and well-based (e.g., SMART-seq)
        platforms.
        
        For details of xcltk and XClone, please checkout our paper:
        
        > Huang, R., Huang, X., Tong, Y. et al. Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone. Nat Commun 15, 6684 (2024). https://doi.org/10.1038/s41467-024-51026-0
        
        
        ## News
        
        You can find the full manual of the xcltk preprocessing pipeline at
        [preprocess/README.md][preprocess manual].
        
        All release notes are available at [docs/release.rst][release]
        
        
        ## Installation
        
        ### Install via pip (latest stable version)
        
        xcltk is avaliable through [pypi][pypi].
        
        ```shell
        pip install -U xcltk
        ```
        
        ### Install from this Github Repo (latest stable/dev version)
        
        ```shell
        pip install -U git+https://github.com/hxj5/xcltk
        ```
        
        In either case, if you don't have write permission for your current Python
        environment, we suggest creating a separate [conda][conda] environment 
        or add `--user` for your current one.
        
        
        ## Manual
        
        You can check the full parameters with `xcltk -h`.
        
        ```
        Program: xcltk (Toolkit for XClone Preprocessing)
        Version: 0.5.2
        
        Usage:   xcltk <command> [options]
        
        Commands:
          -- BAF calculation
             baf              Preprocessing pipeline for XClone BAF.
             fixref           Fix REF allele mismatches based on reference FASTA.
        
          -- RDR calculation
             basefc           Basic feature counting.
        
          -- Tools
             convert          Convert between different formats of genomic features.
        
          -- Others
             -h, --help       Print this message and exit.
             -V, --version    Print version and exit.
        ```
        
        
        
        [conda]: https://docs.conda.io/en/latest/
        [licence]: https://github.com/hxj5/xcltk
        [preprocess manual]: https://github.com/hxj5/xcltk/tree/master/preprocess
        [pypi]: https://pypi.org/project/xcltk
        [release]: https://github.com/hxj5/xcltk/blob/master/docs/release.rst
        [XClone repo]: https://github.com/single-cell-genetics/XClone
        [xcltk repo]: https://github.com/hxj5/xcltk
        
Keywords: xclone,toolkit
Platform: UNKNOWN
Description-Content-Type: text/markdown
