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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. You can also get it from apt, conda or brew.

    If GSL is not installed in the default path,

    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:

    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:

    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 [email protected]

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 http://www.gnu.org/licenses/.