milospjanic
MS in Molecular Biology, Un. Belgrade, Serbia. PhD in Life Sciences, Un. Lausanne, Switzerland. Postdoctoral Fellow, Department of Medicine, Stanford Un, CA, US
Stanford University, School of MedicineStanford, CA.
Pinned 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.
ChIPSeqFPro
ChIPSeqFPro (beta) is a script for full processing of ChIPSeq data starting from fastq files. It performs fastqc quality control, mapping to the human genome hg19 or mouse mm10 using bwa, sam to bam conversion, peak calling with MACS, creates bigwig files from bam files using bam2bigwig.
chrPos2rsID
chrPos2rsID is a script to convert a list of genomics positions in a format: chrno_position_allele1_allele2 to SNP rsIDs. Script will append rsIDs as a column to an existing file. chrPos2rsID is useful for quick conversion of to SNP rsIDs for various downstream analysis and lookups.
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.
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.
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.
IntegrativeFunctionalGenomics
Collection of scripts used in Miller and Pjanic et al, 2016, Nature Communications and Kim and Pjanic et al, 2017, Plos Genetics.
matrixeQTL2LocusZoom
Script will use three parameters as inputs, 1) Gene ID from ENSEMBL annotation, 2) chromosome number where the gene is located 3) eQTL file from matrixeQTL and generate output for visualization with LocusZoom Plot containing rsIDs and p-values as columns 1 and 2.
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.
rsID2Bed
rsID2Bed is a script to convert SNP rsIDs to a list of genomics positions in a bed format: chr, position, position+1. Script is useful for quick conversion of SNPs to a bed format for downstream analysis (e.g. overlaps with bedtools).
milospjanic's Repositories
milospjanic/sam2BigWig
Convert SAM files to BIGWIG files. This script will take a sam file mapped to the human genome hg19 and convert it to a bigwig file for UCSC Genome Browser. Dependencies samtools, bedtools bamtobed, downloads/executes bedItemOverlapCount, bedGraphToBigWig and fetchChromSizes.
milospjanic/bamsplit2bigwig
Convert bam file mapped to the human genome hg19 to two strand specific bigwig files for UCSC Genome Browser. Useful to visualize nucleosomal or protein binding ChIP-Seq 'footprints' marked by reads mapping on different DNA strands. Bamsplit2bigwig depends on bedtools bamtobed, bedItemOverlapCount, bedGraphToBigWig and fetchChromSizes.
milospjanic/tabsep
Formatting of multiple spaces and tabs to a single tab, useful for for quick table formatting.