Milos Pjanic's repositories
bigWigLiftOver
bigWigLiftOver will convert genomics coordinates of a bigwig file mapped to hg18 genome to the hg19 genome, via converting bigwig to bedgraph, and performing liftover, followed by conversion back of a bedgraph to bigwig.
FibonacciLoop
Python script for printing Fibonacci sequence numbers. up to n-th term where n is provided by the user, using looping
gwasCatalog2BedParse
Parse complete GWAS Catalog into unique categories and create bed files. Script will connect to genome.gov, download GWAS Catalog, convert it to a bed file with columns chr;position;position+1;proxy_gene;phenotype, and then create separate bed files for each unique GWAS Catalog category from 5th column.
gwasanalytics
Gwasanalytics consists of a series of scripts that will analyze Gwas Catalog phenotypes and the input bed file from e.g. ChIP-Seq/ATAC-Seq experiment. Gwasanalytics scripts will calculate standard and modified binomial statistics, p-values and fold change for genomic overlaps between the input and various parsed GWAS categories.
rnaSeqFPro
rnaSeqFPro (beta) is a script for full processing of RNASeq data starting from fastq files. It performs fastqc quality control, mapping to the human genome hg19 using STAR second pass, counting with featurecounts using GENCODE gtf annotation, creates master table, performs differential analysis using DESeq2, generates graphs in gglot2.
gwasCatalogFullParseBinomialMod1Ggplot
Script downloads GWAS Catalog, converts it into bed file with columns: chr position position+1 proxy_gene phenotype, then fully parses GWAS Cat. for each unique category, performs modified binomial statistics on overlaps with the input file. Outputs are tables with binomial -log10pvalues and fold changes and graphs in ggplot2.
bed2GwasCatalogBinomialMod1
This is a modified version of bed2GwasCatalogBinomial script and it calculates binomial p-value for genomics overlaps using modified binomial probability. This script will download GWAS Catalog, parse to bed files using input terms, intersects parsed GWAS Catalog with input bed file, calculates modified binomial statistics for each overlap.
bed2GwasCatalogBinomial
Script will download GWAS Catalog, create bed file, parse and uniq with N-1 input arguments. Last argument provided should be a bed file that will be intersected with parsed GWAS Catalog. Number of overlaps and initial number of entries in parsed files are reported. Finally, it will calculate binomial p-values for each overlap.
gwasCatalog2Bed2Category
Download GWAS Catalog, convert it to a bed file with "chr position position+1 proxy_gene phenotype", and then take input terms and select entries that match the term, and create separate bed files.
FibonacciRecursion
Python script for printing Fibonacci sequence numbers. up to n-th term where n is provided by the user, using recursion
DNAPalindromeRevPalindrome
Python script to check if DNA sequence is palindrome or reverse palindrome
PolygenicScoreCAD
PolygenicScoreCAD is a bash/awk/R script for defining causality of a gene for coronary artery disease given the directionality of expression change in HCASMC with the increased global polygenic risk score. Script uses CAD GWAS data (Nelson et al.) and HCASMC eQTL data for regression analysis.
GeneCausalityTestCAD
GeneCausalityTest for CAD (coronary artery disease) is a bash/awk/R script for defining causality of a gene for a given trait, in this case CAD, given the directionality of expression change with the increasing number of risk SNPs. Script uses CAD GWAS data (Nelson et al.) and HCASMC eQTL data for regression analysis.
UniqueHaplotypeTestCAD
UniqueHaplotypeTestCAD is a version of GeneCausalityTest for coronary artery disease that resolves local haplotype structure and averages on samples with unique haplotype structure. The script improves correlations made by GeneCausalityTest for defining causality of a gene for CAD, especially in the local regions of strong linkage disequilibrium. The script outputs the directionality of expression change with the increasing number of risk SNPs and uses CAD GWAS data (Nelson et al.) and HCASMC eQTL data for regression analysis.
SingleCellPCAplotMultiGene
SingleCellPCAplotMultiGene is an R script for the principal component analysis of single cell RNAseq data. The script will start from the processed mastertable with RPKM values and perform PCA clustering and highlight in a gradient scale the ratio of expression of the 2 genes of interest (provided as the first and second arguments).
GTExExtractor.2
GTExExtractor.2 is a script that will download and parse individual-level GTEx data set for all tissues and GTEx sample IDs. It will show the distribution of expression for a single gene in a multiple GTEx tissue that are selected by the user, and the script will automate this process for a list of input genes.
HCASMCeQTLviewer
HCASMCeQTLviewer is a combined bash/R/awk script to view eQTL box/dot plots for a specific gene/SNP cis and trans eQTL association in human coronary artery smooth muscle cells, one of the crucial cell types that are involved in atherosclerotic process of the blood vessel.
ChIPSeqCompare
ChIPSeqCompare is a combined bash/R script that compares two ChIPSeq data sets, calculates overlapping regions and provides distributions of normalized fold change for overlapping binding sites. It outputs a normalized fold change correlation plot indicating either synergistic or antagonistic binding of two factors, or absence of interaction.
fisherTestForGenomicOverlapsMilosPjanicMod
Combined bash/R script performs specialized Fisher's exact test and generates p-value that shows significance for the overlap of two sets of genomic regions. Statistical test includes genomic background i.e. combined ENCODE set of open chromatin regions to calculate constituents of the Fisher exact test contingency matrix.
findLDSNPs
findLDSNPs is a bash/mySQL/awk script to obtain SNPs that are in linkage disequilibrium (LD) with the input list of SNPs using a user defined R2 or dprime value in user defined window around the SNP location. LD calculation is based on 1000Genomes phase 3 phased genomes.
chrPos2rsIDdbSNP147CommonPlusRareVariants
This is a script to convert a list of genomics positions in a format: chrno_position_allele1_allele2 to SNP rsIDs, using dbSNP147 all SNP (common plus rare) data set from UCSC Table Browser. Script will append rsIDs as a column to an existing file.
indelsconverterdbSNP150
chrN:position:I or chrN:position:D to SNP rsIDs, using dbSNP150 all SNP (common plus rare) data set from UCSC Table Browser. Script will append rsIDs as a column to an existing file.
wig2BigWigLiftOverBedgraphPartition
This is a combined bash/perl script that will convert genomics coordinates of a wig file mapped to hg18 genome to the hg19 genome, via converting wig ti bigwig, bigwig to bedgraph, and performing liftover, followed by partitioning the structure of overlapping intervals in a bedgraph file and conversion back of a bedgraph to bigwig.