| Name | counhto JSON |
| Version |
1.1.0
JSON |
| download |
| home_page | |
| Summary | Python package for generating and demultiplexing hash tag oligo count matrices from cellranger output |
| upload_time | 2023-04-07 16:19:29 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.10 |
| license | MIT License Copyright (c) 2023 Daniel Malzl Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
bioinformatics
single cell sequencing
sequencing
ngs
hashtag oligo counting
hashtag oligo demultiplexing
cellranger
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# counhto
An easy to use tool to count hashtag oligos (HTOs) from 10x cellranger count output processed with Antibody Captures for sample multiplexing and assign tags to cells using the cellranger Jibes algorithm (this part is a minimal edit of the original algorithm as implemented in cellranger > 6.0)
## Install
The most convenient and easy way to install the package is
```
pip install countho
```
alternatively you could also clone the repository and install it manually like
```
git clone git@github.com:dmalzl/counhto.git
cd countho
pip install .
```
## Usage
Using it is as simple as setting up a csv file with the following structure
|bamfile|barcodefile|htofile|outputdir|
|:------|:----------|:------|:--------|
|cellranger/outs/possorted_bam.bam|cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz|cellranger/outs/feature_ref.csv|/path/to/outputdir/|
|cellranger/outs/possorted_bam.bam|cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz|cellranger/outs/feature_ref.csv|/path/to/outputdir/|
and invoking countho as follows
```
countho --csv sample_csv.csv [-p n]
```
The `-p` argument specifies the number of cpus to use for processing however this only has an effect if more than one samples are supplied.
counhto then counts UMIs per HTO and automatically performes tag assignment using cellrangers Jibes algoritm (see [cell multiplexing documentation](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/cellplex) for more info). The output for each sample will then be written to the specified output directories where the barcodes.tsv file contains the tag assignment information. The directory has following structure
```
/path/to/outputdir/
|__
|__barcodes.tsv # filtered barcodes with tag assignment information
|__features.tsv # names of the HTOs as specified in the feature_ref.csv file
|__matrix.mtx # MatrixMarket formated count matrix of shape n_barcodes x n_HTOs
```
Raw data
{
"_id": null,
"home_page": "",
"name": "counhto",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.10",
"maintainer_email": "",
"keywords": "bioinformatics,single cell sequencing,sequencing,NGS,hashtag oligo counting,hashtag oligo demultiplexing,cellranger",
"author": "",
"author_email": "Daniel Malzl <daniel@menchelab.com>",
"download_url": "https://files.pythonhosted.org/packages/7b/1d/25d606daddd0f5a2627dc94529cd64701705b8c7a474c8e42d3bfcb3a7fc/counhto-1.1.0.tar.gz",
"platform": null,
"description": "# counhto\n\n\n\nAn easy to use tool to count hashtag oligos (HTOs) from 10x cellranger count output processed with Antibody Captures for sample multiplexing and assign tags to cells using the cellranger Jibes algorithm (this part is a minimal edit of the original algorithm as implemented in cellranger > 6.0)\n\n## Install\nThe most convenient and easy way to install the package is\n```\npip install countho\n```\n\nalternatively you could also clone the repository and install it manually like\n```\ngit clone git@github.com:dmalzl/counhto.git\ncd countho\npip install .\n```\n\n## Usage\nUsing it is as simple as setting up a csv file with the following structure\n|bamfile|barcodefile|htofile|outputdir|\n|:------|:----------|:------|:--------|\n|cellranger/outs/possorted_bam.bam|cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz|cellranger/outs/feature_ref.csv|/path/to/outputdir/|\n|cellranger/outs/possorted_bam.bam|cellranger/outs/filtered_feature_bc_matrix/barcodes.tsv.gz|cellranger/outs/feature_ref.csv|/path/to/outputdir/|\n\nand invoking countho as follows\n```\ncountho --csv sample_csv.csv [-p n]\n```\n\nThe `-p` argument specifies the number of cpus to use for processing however this only has an effect if more than one samples are supplied.\n\ncounhto then counts UMIs per HTO and automatically performes tag assignment using cellrangers Jibes algoritm (see [cell multiplexing documentation](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/cellplex) for more info). The output for each sample will then be written to the specified output directories where the barcodes.tsv file contains the tag assignment information. The directory has following structure\n```\n/path/to/outputdir/\n|__\n |__barcodes.tsv # filtered barcodes with tag assignment information\n |__features.tsv # names of the HTOs as specified in the feature_ref.csv file\n |__matrix.mtx # MatrixMarket formated count matrix of shape n_barcodes x n_HTOs\n```\n",
"bugtrack_url": null,
"license": "MIT License Copyright (c) 2023 Daniel Malzl Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ",
"summary": "Python package for generating and demultiplexing hash tag oligo count matrices from cellranger output",
"version": "1.1.0",
"split_keywords": [
"bioinformatics",
"single cell sequencing",
"sequencing",
"ngs",
"hashtag oligo counting",
"hashtag oligo demultiplexing",
"cellranger"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "cab39027ccd1a4657d8297fe6cb48d2f3871f434419d9dffab5e52c39f83362e",
"md5": "49dfca09dcc986ec713c8f396b058ad1",
"sha256": "ef8a167d0975d10d8a8d1f50c2db7cfa4a82de3b9efb79161b82bf485dd78857"
},
"downloads": -1,
"filename": "counhto-1.1.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "49dfca09dcc986ec713c8f396b058ad1",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.10",
"size": 24911,
"upload_time": "2023-04-07T16:19:26",
"upload_time_iso_8601": "2023-04-07T16:19:26.993187Z",
"url": "https://files.pythonhosted.org/packages/ca/b3/9027ccd1a4657d8297fe6cb48d2f3871f434419d9dffab5e52c39f83362e/counhto-1.1.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "7b1d25d606daddd0f5a2627dc94529cd64701705b8c7a474c8e42d3bfcb3a7fc",
"md5": "457a5da4c0c4ce04f429494c796739c9",
"sha256": "2acdd4a70edfa2a648f3ee385ca0040b0d1970ad1fc79229ac565fbd1cbcd0df"
},
"downloads": -1,
"filename": "counhto-1.1.0.tar.gz",
"has_sig": false,
"md5_digest": "457a5da4c0c4ce04f429494c796739c9",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.10",
"size": 22298,
"upload_time": "2023-04-07T16:19:29",
"upload_time_iso_8601": "2023-04-07T16:19:29.074276Z",
"url": "https://files.pythonhosted.org/packages/7b/1d/25d606daddd0f5a2627dc94529cd64701705b8c7a474c8e42d3bfcb3a7fc/counhto-1.1.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-04-07 16:19:29",
"github": false,
"gitlab": false,
"bitbucket": false,
"lcname": "counhto"
}
