| Name | pyGeneEnrich JSON |
| Version |
0.0.2
JSON |
| download |
| home_page | None |
| Summary | A limited python implementation of clusterProfiler from R |
| upload_time | 2024-04-07 07:33:45 |
| maintainer | None |
| docs_url | None |
| author | WhiteRabBio |
| requires_python | >=3.9 |
| license | MIT License Copyright (c) 2024 WhiteRabBio 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 |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
pandas
numpy
scipy
statsmodels
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
GeneEnrich
==========
Installation and Usage
----------------------
##### Manual installation (Without Update Database Function)
~~~~~~~~~~~~~~~~~~~bash
The recommended installation is as follows:
.. code-block:: bash
(GeneEnrich) $ pip install GeneEnrich
~~~~~~~~~~~~~~~~~~~
##### Manual installation
~~~~~~~~~~~~~~~~~~~bash
The recommended installation is as follows:
conda_pkgs.txt can be found in https://github.com/WhiteRabBio/GeneEnrich
.. code-block:: bash
(GeneEnrich) $ mamba create -n GeneEnrich -y --file conda_pkgs.txt
(GeneEnrich) $ pip install GeneEnrich
~~~~~~~~~~~~~~~~~~~
##### Usage
```bash
usage: GeneEnrich run_go [-h] --input INPUT_FILE --prefix PREFIX --output OUTPUT_DIR --species SPECIES --type
{scanpy_deg,seuratv3_deg,seuratv4_deg,list} [--updown {up,down,both}] [--pvalue PVALUE] [--qvalue QVALUE]
Run enrichment based on GO database.
options:
-h, --help show this help message and exit
--input INPUT_FILE Choosen from `Differential Expression Gene file generated by Scanpy or Seurat` And `One column gene list
--prefix PREFIX Prefix of output results.
--output OUTPUT_DIR Output file location.
--species SPECIES Support human or mouse.
--type {scanpy_deg,seuratv3_deg,seuratv4_deg,list}
DEG file or Gene list file
--updown {up,down,both}
Use up-regulated gene\down-regulated gene\ both, if DEG provided.
--pvalue PVALUE Pvalue cutoff for enrichment
--qvalue QVALUE Qvalue cutoff for enrichment
```
```bash
usage: GeneEnrich run_kegg [-h] --input INPUT_FILE --prefix PREFIX --output OUTPUT_DIR --species SPECIES --type
{scanpy_deg,seuratv3_deg,seuratv4_deg,list} [--updown {up,down,both}] [--pvalue PVALUE] [--qvalue QVALUE]
Run enrichment based on KEGG database.
options:
-h, --help show this help message and exit
--input INPUT_FILE Choosen from `Differential Expression Gene file generated by Scanpy or Seurat` And `One column gene list
--prefix PREFIX Prefix of output results.
--output OUTPUT_DIR Output file location.
--species SPECIES Support human or mouse.
--type {scanpy_deg,seuratv3_deg,seuratv4_deg,list}
DEG file or Gene list file
--updown {up,down,both}
Use up-regulated gene\down-regulated gene\ both, if DEG provided.
--pvalue PVALUE Pvalue cutoff for enrichment
--qvalue QVALUE Qvalue cutoff for enrichment
```
```bash
usage: GeneEnrich update_db [-h] --database {KEGG,GO} --species SPECIES --version {python,R}
Update GO and KEGG database.
options:
-h, --help show this help message and exit
--database {KEGG,GO} Choosen from KEGG or GO database to update.
--species SPECIES Support human or mouse.
--version {python,R} If python, will download latest database from website. If R, will extract database from existing database
info.
```
##### Citation
Yu, Guangchuang et al. “clusterProfiler: an R package for comparing biological themes among gene clusters.” *Omics : a journal of integrative biology* vol. 16,5 (2012): 284-7. doi:10.1089/omi.2011.0118
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"description": "GeneEnrich\n==========\n\nInstallation and Usage\n----------------------\n\n##### Manual installation (Without Update Database Function)\n\n~~~~~~~~~~~~~~~~~~~bash\n\nThe recommended installation is as follows:\n\n.. code-block:: bash\n\n (GeneEnrich) $ pip install GeneEnrich\n\n~~~~~~~~~~~~~~~~~~~\n\n##### Manual installation\n\n~~~~~~~~~~~~~~~~~~~bash\nThe recommended installation is as follows:\nconda_pkgs.txt can be found in https://github.com/WhiteRabBio/GeneEnrich\n\n.. code-block:: bash\n\n (GeneEnrich) $ mamba create -n GeneEnrich -y --file conda_pkgs.txt\n (GeneEnrich) $ pip install GeneEnrich\n\n~~~~~~~~~~~~~~~~~~~\n\n##### Usage\n\n```bash\nusage: GeneEnrich run_go [-h] --input INPUT_FILE --prefix PREFIX --output OUTPUT_DIR --species SPECIES --type\n {scanpy_deg,seuratv3_deg,seuratv4_deg,list} [--updown {up,down,both}] [--pvalue PVALUE] [--qvalue QVALUE]\n\nRun enrichment based on GO database.\n\noptions:\n -h, --help show this help message and exit\n --input INPUT_FILE Choosen from `Differential Expression Gene file generated by Scanpy or Seurat` And `One column gene list\n --prefix PREFIX Prefix of output results.\n --output OUTPUT_DIR Output file location.\n --species SPECIES Support human or mouse.\n --type {scanpy_deg,seuratv3_deg,seuratv4_deg,list}\n DEG file or Gene list file\n --updown {up,down,both}\n Use up-regulated gene\\down-regulated gene\\ both, if DEG provided.\n --pvalue PVALUE Pvalue cutoff for enrichment\n --qvalue QVALUE Qvalue cutoff for enrichment\n\n```\n\n\n\n```bash\nusage: GeneEnrich run_kegg [-h] --input INPUT_FILE --prefix PREFIX --output OUTPUT_DIR --species SPECIES --type\n {scanpy_deg,seuratv3_deg,seuratv4_deg,list} [--updown {up,down,both}] [--pvalue PVALUE] [--qvalue QVALUE]\n\nRun enrichment based on KEGG database.\n\noptions:\n -h, --help show this help message and exit\n --input INPUT_FILE Choosen from `Differential Expression Gene file generated by Scanpy or Seurat` And `One column gene list\n --prefix PREFIX Prefix of output results.\n --output OUTPUT_DIR Output file location.\n --species SPECIES Support human or mouse.\n --type {scanpy_deg,seuratv3_deg,seuratv4_deg,list}\n DEG file or Gene list file\n --updown {up,down,both}\n Use up-regulated gene\\down-regulated gene\\ both, if DEG provided.\n --pvalue PVALUE Pvalue cutoff for enrichment\n --qvalue QVALUE Qvalue cutoff for enrichment\n\n```\n\n\n\n```bash\nusage: GeneEnrich update_db [-h] --database {KEGG,GO} --species SPECIES --version {python,R}\n\nUpdate GO and KEGG database.\n\noptions:\n -h, --help show this help message and exit\n --database {KEGG,GO} Choosen from KEGG or GO database to update.\n --species SPECIES Support human or mouse.\n --version {python,R} If python, will download latest database from website. If R, will extract database from existing database\n info.\n```\n\n\n\n##### Citation\n\nYu, Guangchuang et al. \u201cclusterProfiler: an R package for comparing biological themes among gene clusters.\u201d *Omics : a journal of integrative biology* vol. 16,5 (2012): 284-7. doi:10.1089/omi.2011.0118\n",
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