# xcltk: Toolkit for XClone Preprocessing
[][pypi]
[][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.
## 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: 0.4.0
Usage: xcltk <command> [options]
Commands:
-- BAF calculation
allelefc Allele-specific feature counting.
baf Preprocessing pipeline for XClone BAF.
fixref Fix REF allele mismatches based on reference FASTA.
rpc Reference phasing correction.
-- 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
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"description": "# xcltk: Toolkit for XClone Preprocessing\n\n[][pypi]\n[][licence]\n\n\n[XClone][XClone repo] is a statistical method to detect allele- and \nhaplotype-specific copy number variations (CNVs) and reconstruct \ntumour clonal substructure from scRNA-seq data, \nby integrating the expression levels (read depth ratio; RDR signals) and \nthe allelic balance (B-allele frequency; BAF signals).\nIt takes three matrices as input: the allele-specific *AD* and *DP* matrices\n(BAF signals) and the *total read depth* matrix (RDR signals).\n\nThe [xcltk][xcltk repo] package implements a preprocessing pipeline to \ngenerate the three matrices from SAM/BAM/CRAM files.\nIt supports data from multiple single-cell sequencing platforms, including \ndroplet-based (e.g., 10x Genomics) and well-based (e.g., SMART-seq)\nplatforms.\n\n\n## News\n\nYou can find the full manual of the xcltk preprocessing pipeline at\n[preprocess/README.md][preprocess manual].\n\nAll release notes are available at [docs/release.rst][release]\n\n\n## Installation\n\n### Install via pip (latest stable version)\n\nxcltk is avaliable through [pypi][pypi].\n\n```shell\npip install -U xcltk\n```\n\n### Install from this Github Repo (latest stable/dev version)\n\n```shell\npip install -U git+https://github.com/hxj5/xcltk\n```\n\nIn either case, if you don't have write permission for your current Python\nenvironment, we suggest creating a separate [conda][conda] environment \nor add `--user` for your current one.\n\n\n## Manual\n\nYou can check the full parameters with `xcltk -h`.\n\n```\nProgram: xcltk (Toolkit for XClone Preprocessing)\nVersion: 0.4.0\n\nUsage: xcltk <command> [options]\n\nCommands:\n -- BAF calculation\n allelefc Allele-specific feature counting.\n baf Preprocessing pipeline for XClone BAF.\n fixref Fix REF allele mismatches based on reference FASTA.\n rpc Reference phasing correction.\n\n -- RDR calculation\n basefc Basic feature counting.\n\n -- Tools\n convert Convert between different formats of genomic features.\n\n -- Others\n -h, --help Print this message and exit.\n -V, --version Print version and exit.\n```\n\n\n\n[conda]: https://docs.conda.io/en/latest/\n[licence]: https://github.com/hxj5/xcltk\n[preprocess manual]: https://github.com/hxj5/xcltk/tree/master/preprocess\n[pypi]: https://pypi.org/project/xcltk\n[release]: https://github.com/hxj5/xcltk/blob/master/docs/release.rst\n[XClone repo]: https://github.com/single-cell-genetics/XClone\n[xcltk repo]: https://github.com/hxj5/xcltk\n",
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