Pinned Repositories
PairedEndAssemblyConda
Worflow performing de novo assembly of bacterial genomes from paired-end reads
PairedEndVariantConda
Workflow performing variant calling analysis of bacterial genomes from paired-end reads
BashDataManagement
Useful Bash commands to manage genomics data and dataframes from multiple sources
cgMLSTcomparison
Script performing Principal Component Analysis (PCA) and Generalized Linear Model (GLM)
DownsampledReads
Script performing 4-way figures and linear regressions
TreeToCongruency
Script comparing two trees through a tanglegram and estimations of congruency metrics
PairwiseDifferencesToROC
Script performing Receiver Operating Characteristic (ROC) analysis to identify thresholds of mutation pairwise differences from microbial genomes involved in an investigated outbreak
PairwiseDifferencesToNonParametric
Script performing non-parametric tests (i.e. Kolmogorov, Kruskal and Wilcoxon) between mutation pairwise differences from microbial genomes involved in an investigated outbreak
SingleLinkageToPairwiseThresholds
Script identifying relationship between thresholds of pairwise differences and single linkage
VariantAlignmentConda
Workflow performing variant compilation of bacterial genomes from varaint calling analysis
Nicolas-Radomski's Repositories
Nicolas-Radomski/canSNPtyping
Scripts building schemes of canonical SNPs based on feht output and compatible with hansel input
Nicolas-Radomski/GenomicBasedMachineLearning
Workflow solving balanced or unbalanced multiclass phenotypes from binary and categorical genomic profiles
Nicolas-Radomski/TreeToCongruency
Script comparing two trees through a tanglegram and estimations of congruency metrics
Nicolas-Radomski/StatisticalRelationships
Scripts computing correlations or associations from numerical or categorical variables
Nicolas-Radomski/AccurateGenomicElements
Script calculating accuracy of mutation profiles between two groups of samples
Nicolas-Radomski/SingleLinkageToPairwiseThresholds
Script identifying relationship between thresholds of pairwise differences and single linkage
Nicolas-Radomski/PairwiseDifferencesToROC
Script performing Receiver Operating Characteristic (ROC) analysis to identify thresholds of mutation pairwise differences from microbial genomes involved in an investigated outbreak
Nicolas-Radomski/DownsampledReads
Script performing 4-way figures and linear regressions
Nicolas-Radomski/cgMLSTcomparison
Script performing Principal Component Analysis (PCA) and Generalized Linear Model (GLM)
Nicolas-Radomski/PairwiseDifferencesToNonParametric
Script performing non-parametric tests (i.e. Kolmogorov, Kruskal and Wilcoxon) between mutation pairwise differences from microbial genomes involved in an investigated outbreak
Nicolas-Radomski/BashDataManagement
Useful Bash commands to manage genomics data and dataframes from multiple sources
Nicolas-Radomski/VariantAlignmentConda
Workflow performing variant compilation of bacterial genomes from varaint calling analysis
Nicolas-Radomski/PairedEndVariantConda
Workflow performing variant calling analysis of bacterial genomes from paired-end reads
Nicolas-Radomski/VariantFastaConda
Workflow producing a multi-fasta file for downstream bacterial phylogenomic analyses from variant calling analysis
Nicolas-Radomski/PairedEndAssemblyConda
Worflow performing de novo assembly of bacterial genomes from paired-end reads