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dart-id-2.0.7
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مشاهده بیشترتوضیحات
RT Alignment and Peptide ID Confidence Updating for LC-MS/MS Data
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | dart-id-2.0.7 |
| نام | dart-id |
| نسخه کتابخانه | 2.0.7 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Albert Chen |
| ایمیل نویسنده | chen.alb@husky.neu.edu |
| آدرس صفحه اصلی | https://github.com/SlavovLab/DART-ID |
| آدرس اینترنتی | https://pypi.org/project/dart-id/ |
| مجوز | MIT |
# DART-ID
Website: [https://dart-id.slavovlab.net](https://dart-id.slavovlab.net)
Manuscript: [https://www.biorxiv.org/content/10.1101/399121v3](https://www.biorxiv.org/content/10.1101/399121v3)
----------
## Getting started
### Dependencies
DART-ID requires Python >= 3.4 (64-bit - [miniconda distribution recommended](https://docs.conda.io/en/latest/miniconda.html)), and has been tested on Windows 8 / OSX Mojave 10.14 / Centos 7 / Ubuntu 14.04.
### Installation
DART-ID is available on [PyPI](https://pypi.org/project/dart-id/) and can be installed with [pip](https://pip.pypa.io/en/stable/installing/).
```bash
pip install dart-id
```
### Usage
DART-ID requires a YAML-formatted configuration file to run. An example annotated config file can be found in [example/config_annotated.yaml](https://github.com/SlavovLab/DART-ID/blob/master/example/config_annotated.yaml). You can specify input files and the output folder on the command line, if that's what you prefer.
View the command-line arguments anytime by running: ```dart_id -h```.
```
usage: dart_id [-h] [-i INPUT [INPUT ...]] [-o OUTPUT] [-v] [--version] -c
CONFIG_FILE
optional arguments:
-h, --help show this help message and exit
-i INPUT [INPUT ...], --input INPUT [INPUT ...]
Input file(s) from search engine output (e.g.,
MaxQuant evidence.txt). Not required if input files
are specified in the config file
-o OUTPUT, --output OUTPUT
Path to output folder
-v, --verbose
--version Display the program's version
-c CONFIG_FILE, --config-file CONFIG_FILE
Path to config file (required). See
example/config_example.yaml
```
### Example runs
An example configuration file can be downloaded from GitHub: [https://github.com/SlavovLab/DART-ID/blob/master/config_files/example_sqc_67_95_varied.yaml](https://raw.githubusercontent.com/SlavovLab/DART-ID/master/config_files/example_sqc_67_95_varied.yaml).
The first few lines of the above configuration file specify the path to the input file:
```yaml
## Input
## ==========================
input:
- /path/to/SQC_67_95_Varied/evidence.txt
```
You can download the ```evidence.txt``` file from MassIVE: [ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/evidence.txt](ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/evidence.txt).
Then edit the path to the file downloaded, and run the following command:
```bash
dart_id -c config_files/example_sqc_67_95_varied.yaml -o ~/DART_ID/SQC_67_95_varied_20181206
```
The ```-o``` parameter points to the output folder for DART-ID. You can also specify this path in the config file.
An example analysis of the data and configuration file specified above is available publicly at [ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/](ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/).
---
## About the project
DART-ID is a project developed in the [Slavov Laboratory](https://web.northeastern.edu/slavovlab/) at [Northeastern University](https://www.northeastern.edu/) [Bioengineering](http://www.bioe.neu.edu/), and was authored by [Albert Tian Chen](https://atchen.me), [Alexander Franks](http://afranks.com/) (of [UCSB Statistics and Applied Probability](https://www.pstat.ucsb.edu/)), and [Nikolai Slavov](https://web.northeastern.edu/slavovlab/).
The manuscript for this tool is available on bioRxiv: [https://www.biorxiv.org/content/10.1101/399121v3](https://www.biorxiv.org/content/10.1101/399121v3).
Contact the authors by email: [nslavov\{at\}northeastern.edu](mailto:nslavov@northeastern.edu).
### License
DART-ID is distributed by an [MIT license](https://github.com/SlavovLab/DART-ID/blob/master/LICENSE.txt).
### Contributing
Please feel free to contribute to this project by opening an issue or pull request in the [GitHub repository](https://github.com/SlavovLab/DART-ID).
### Data
All data used for the manuscript is available on [UCSD's MassIVE Repository](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ed5a1ab37dc34985bbedbf3d9a945535)
### Figures/Analysis
Scripts for the figures in the DART-ID manuscript are available in a separate GitHub repository, [https://github.com/SlavovLab/DART-ID_2018](https://github.com/SlavovLab/DART-ID_2018)
نیازمندی
| مقدار | نام |
|---|---|
| <2.3,>=2.1 | networkx |
| >=3.0.1 | jsonschema |
| >=3.12 | pyyaml |
| >=1.14.3 | numpy |
| >=1.0.0 | scipy |
| >=0.22.0 | pandas |
| >=2.1.2 | matplotlib |
نحوه نصب
نصب پکیج whl dart-id-2.0.7:
pip install dart-id-2.0.7.whl
نصب پکیج tar.gz dart-id-2.0.7:
pip install dart-id-2.0.7.tar.gz