https://github.com/smithlabcode/cread
Software tools for regulatory sequence analysis
https://github.com/smithlabcode/cread
Last synced: 6 months ago
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Software tools for regulatory sequence analysis
- Host: GitHub
- URL: https://github.com/smithlabcode/cread
- Owner: smithlabcode
- License: gpl-3.0
- Created: 2020-03-10T00:22:24.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2023-11-29T22:06:21.000Z (over 2 years ago)
- Last Synced: 2025-04-01T00:29:55.507Z (about 1 year ago)
- Language: C++
- Homepage:
- Size: 360 KB
- Stars: 0
- Watchers: 7
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# cread
Software tools for regulatory sequence analysis
CREAD: Comprehensive Regulatory Element Analysis and Discovery. The
CREAD software package is a computational pipeline for understanding
how DNA and RNA elements participate in regulating gene expression.
CREAD uses Pattern-Feature-Model framework for setting up analyses
with machine learning and pattern visualization to identify motifs
involved in transcriptional regulation. CREAD also includes code
libraries to facilitate implementation of new tools.
Building and Installing
=======================
This software has been designed to run in a UNIX-like environment.
* Step 1
This software package requires a functioning installation of the GNU
Scientific Library (GSL). If you don't already have this installed,
you can download it [here](http://www.gnu.org/software/gsl/). You can
also get it from apt, conda or brew.
If GSL is not installed in the default path,
```console
export CPATH=/path_to_my_gsl/include
export LIBRARY_PATH=/path_to_my_gsl/lib
```
will add search paths for compiling and linking.
You will also need to clone this repo recursively to get the source
with submodules:
```console
git clone --recursive https://github.com/smithlabcode/cread.git
```
* Step 2
To build the binaries type the following from the root of the
source tree:
```console
make
make install
```
This will create all of the binaries and then create a `bin`
directory, in the current directory, containing all the binaries.
Contacts and Bug Reports
========================
Andrew D. Smith
andrewds@usc.edu
Copyright and License Information
=================================
Copyright (C) 2005-2023
Andrew D. Smith
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .