Commit 876ea380 authored by Srikanth Ravichandran's avatar Srikanth Ravichandran
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## About
Scripts for the Markovchain model of signal transduction to capture cell subpopulation specific signaling intermediates.
Scripts and associated input data for the Markovchain model of signal transduction to capture cell subpopulation specific signaling intermediates.
### Authors
This was developed in the [Computational Biology Group](https://wwwfr.uni.lu/lcsb/research/computational_biology) by
The Markovchain model and the scripts to generate it was developed in the [Computational Biology Group](https://wwwfr.uni.lu/lcsb/research/computational_biology) by
- [Srikanth Ravichandran](https://wwwen.uni.lu/lcsb/people/srikanth_ravichandran)
- [Antonio del Sol](https://wwwfr.uni.lu/lcsb/people/antonio_del_sol_mesa)
## System requirements
### Hardware requirements
The scripts requires only a standard PC, for optimal performance, at least 8 GB of RAM and 4 cores of 2.5 GHz each (or above) are recommended.
### Software dependencies
The package supports linux and macOS operating systems, and requires `R` version 3.2.3 or later. Tested platforms:
- linux: Ubuntu 16.04 TLS / R 3.2.3
- macOS: Sierra 10.12.6 / R 3.5.1
Running the interface locally requires `RStudio`, we suggest to use the latest build (RStudio Desktop 1.1.463)
## Instruction to use
`Script_markov.R` contains the necessary functions for the Markovchain model. `Run_markov.R` contains the necessary commands to generate the output files.
Each sub-poulation are taken as input and the respective steady state probability distributions are saved in as output as txt files (with format `SS_`).
Comparison among the steady state probability distribution are made to identiy the subpopulation specific intermediates (`SS_all_network_final`). This file contains the final list of subpopulation specific signaling intermediates. For more details refer the original study ....
In order to run the scripts following R packages are required to be installed: `plyr`, `igraph`, `Matrix`, `reshape2`
### Disclaimer
THE SOFTWARE IS NOT TO BE USED FOR TREATING OR DIAGNOSING HUMAN SUBJECTS.
## Disclaimer
THE SOFTWARE AND ALL CONTENT ON THIS SERVER ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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THE SOFTWARE/SCRIPTS AND ALL CONTENT ON THIS SERVER ARE PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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