Martin Sebastijan Šestak's repositories
FindOrigin
Perl modulino used to analyze BLAST output and BLAST database in ClickHouse (columnar DBMS for OLAP and analytics).
PsiBlastHelper
PsiBlastHelper - It's modulino that splits fasta input file into number of chunks for BLAST, PSI-BLAST and HMMER. It also writes SGE and HTCondor scripts to run these jobs on cluster or grid.
BlastoutAnalyze
It's a modulino used to analyze BLAST output and a database for BLAST.
CollectGenomes
Download genomes from Ensembl FTP, NCBI and JGI and build a BLAST database
CompareMaps
CompareMaps - It's an R script to compare two phylostratigraphic maps and visualize this comparison using heatmap.
bluegreen
Simple demo code for Blue Green Deployments
calculate_hypergeometric_test
R script that will calculate log-odds, hypergeometric test, FDR and Bonferroni correction
Domazet-Loso_MBE_2016
Scripts for "No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution"
MySQLinstall
MySQLinstall - is Perl installation script (modulino) that installs MySQL (or Percona MySQL or MariaDB) in a sandbox using MySQL::Sandbox, additional engines like TokuDB and Deep and updates configuration.
Perlinstall
Perlinstall - is installation script (modulino) that installs Perl (or cperl) using plenv. It also installs cpanm with Perl you are installing. If you have sudo permissions it also installs git and your Linux distribution based "Development tools" for you. If you have git, gcc and make you can skip sudo.
StratiphyParallel
StratiphyParallel is modulino to run PhyloStrat in parallel, collect information from maps and run multiple log-odds analyses on them.