diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..0d0304c --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,27 @@ +Copyright (c) 2023, Jan Patrick Pett +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \ No newline at end of file diff --git a/README.md b/README.md index d877dfc..5ce2e24 100644 --- a/README.md +++ b/README.md @@ -1 +1,16 @@ # snp2cell + +snp2cell is a package for identifying gene regulation involved in specific traits and cell types. +It combines three elements: (i) GWAS summary statistics, (ii) single cell data and (iii) a base gene regulatory network. +A network propagation approach is used to integrate and overlap different types of scores on the network. +Random permutations of scores are used to evaluate the significance of high scores. +A networkx graph of the gene regulatory network with integrated scores can be used to inspect gene regulatory programs that are linked to the trait (from GWAS) on a per cell type basis. + +## Installation + +```commandline +mamba create -n snp2cell python<3.12 +mamba activate snp2cell + + +``` \ No newline at end of file