معرفی شرکت ها
coltron-1.0.2
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Package for generating and analyzing transcription networks
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | coltron-1.0.2 |
| نام | coltron |
| نسخه کتابخانه | 1.0.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Alex Federation |
| ایمیل نویسنده | drpolaskijr@gmail.com |
| آدرس صفحه اصلی | https://github.com/BradnerLab/pipeline |
| آدرس اینترنتی | https://pypi.org/project/coltron/ |
| مجوز | UNKNOWN |
Coltron
=======
Overview
--------
Coltron is an application designed to build transcriptional regulatory networks.
Installation
------------
Installation of Coltron has only been vetted on Ubuntu 12.04 LTS and Ubuntu 14.04 LTS. If you encounter \
any errors in the installation process, please contact drpolaskijr@gmail.com for additional help.
**Confirm PIP Installation**::
pip --version
pip 1.5.6 from /usr/local/lib/python2.7/dist-packages/pip-1.5.6-py2.7.egg (python 2.7)
If the pip --version command generates a command not found error, you will have to download PIP. Instructions for the installation can be found at the following `location
<https://pip.pypa.io/en/latest/installing.html>`_.
Run the following command to start the module download::
$ sudo pip install coltron
This command should produce output that looks like this::
$ sudo pip install coltron
Downloading coltron-1.0.1.tar.gz (8.8MB)
100% |████████████████████████████████| 8.8MB 7.3kB/s
Building wheels for collected packages: coltron
Running setup.py bdist_wheel for coltron
Stored in directory: /home/name/.cache/pip/wheels/83/8c/26/def2b761371d20e93848a6628662df
Successfully built coltron
Installing collected packages: coltron
Successfully installed coltron-1.0.1
Once the PIP installation is complete, the data files that Coltron uses to operate must be downloaded.
**Data Download**
Coltron provides a command for downloading its required files. The command can be executed as follows::
$ sudo coltron-get-data
The required data is downloaded from the web and stored in Coltron's data repository. This process can be time consuming.
Usage
-----
The following command is used to run the main Coltron executable::
$ coltron [options] -e [ENHANCER_FILE] -b [BAM_FILE] -g [GENOME] -o [OUTPUTFOLDER] -n [NAME]
Options::
-h HELP, --help show this help message and exit
-e ENHANCERS, --enhancer_file=ENHANCERS
Provide a ROSE generated enhancer table
(_AllEnhancers.table.txt)
-b BAM, --bam=BAM Provide a bam that corresponds to the super enhancer
table
-g GENOME, --genome=GENOME
Provide the build of the genome to be used for the
analysis. Currently supports HG19, HG18 and MM9
-o OUTPUT, --output=OUTPUT
Enter an output folder
-n NAME, --name=NAME Provide a name for the job
-s SUBPEAKS, --subpeaks=SUBPEAKS
Enter a BED file of regions to search for motifs
-x EXPCUTOFF, --expCutoff=EXPCUTOFF
Enter the expression cutoff to be used to define
candidate TFs
-l EXTENSION, --extension-length=EXTENSION
Enter the length to extend subpeak regions for motif
finding
-a ACTIVITY, --activity=ACTIVITY
A table with refseq in the first column and activity
(expression or promoter acetylation) in second
-E ENUMBER, --enhancer_number=ENUMBER
Enter the number of top ranked enhancers to include in
the analysis. Default is all super-enhancers
--promoter=PROMOTER Enter True if the promoters should be included in the
analysis
--motifs=MOTIFS Enter an alternative PWM file for the analysis
-t TFS, --tfs=TFS Enter additional TFs (comma separated) to be used in
the bindinf analysis
-v VALLEY, --valley=VALLEY
Parameter for valley calling threshold, default = 0.3
Dependencies
------------
Coltron has a number of software dependencies for full operation:
`Bamliquidator
<https://github.com/BradnerLab/pipeline/wiki/bamliquidator>`_ – version 1.2.0
`Samtools
<http://samtools.sourceforge.net>`_
– version 0.1.19
`FIMO
<http://meme-suite.org/doc/install.html>`_
– version 4.91
`NetworkX
<https://networkx.github.io>`_
– version 1.8.1
PIP installation will take care of the NetworkX dependency. Installation guides
for the remaining dependencies can be found at the links provided.
نحوه نصب
نصب پکیج whl coltron-1.0.2:
pip install coltron-1.0.2.whl
نصب پکیج tar.gz coltron-1.0.2:
pip install coltron-1.0.2.tar.gz