TEMPLERUN is a comparative and population genomics tool that performs in-depth analyses of the action of constraint and adaptation on the non-coding TFBS elements within the genomes. These elements are identified using TEMPLE
TEMPLRUN is exclusively written in R, with occasional internal calls to external tools (TEMPLE, vcftools, bcftools and vcfkit) that are to be preinstalled. The R libraries required for running TEMPLERUN are listed in temple_run.R.
The tool's centre point is temple_run.R. This script is the import point for libraries and the species-specific input files that will be used later for the analyses. Additionally, this script is also the call point for scripts, stored in includes folder, that perform sequential processing of the input files.
The input points for the species-specific files are documented in temple_run.R. These can be replaced with input files for other species. Example input files are listed in the folder input_files . The resulting output files are listed in example_output folder. Scripts used for performing analyses are listed in analysis folder
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