Variant caller from pileup notation / samtools alignment

Variant annotation of vcf file using exac and vep

Java based implementation of an MLE method using chi square test to calculate interference during meiotic crossover (the number of double strand dna breaks that don't result in a crossover)

Module for tracking tubes and aliquots and assign storage in the freezers ; Part of the MVP specimen processing system VABHS. Prototype

16sRNA Microbial Profiling R scripts to find most significant OTUs in 16RNA data after data normalization, followed by ordination and clustering and then plotting iTOL

Application to view Entrez data (distribution of Hs / Mm genes per chromosome) using RShiny and MongoDB

Python code to compute adatper content in reads, kmer content, per-base-GC content (at a specific position in a read alignment, against reference genome), per base NC content (at a specific positio…

Python code to detect ECGR Mutations; Takes a reference genome and bunch of reads as input and finds mutations (1-3 bp length) where number of supporting reads greater than 5

ETL scripts to populate caBIO database

Kmer counter is written in GO Lang v 1.16.5 To install GO on Windows, follow the instructions at https://golang.org/doc/install 4 GO implementation of N-mer counter in DNA sequences which tests for…

1.Partial Scripts to process sequence clusters from 16000 microbial genomes to find orthologous protein clusters, using the most representative sequence per cluster 2. Find fold distribution across…

Simulation of baseline survey response variables to store information in EPIC Number of variables: 495 Code: Java 8 Reads in csv file of variables and value range of permitted responses Use randomi…

Microarray data analysis using R / BioConductor

Parses Samtools output and extracts flagstat results such as number of reads that are pass/fail that are properly aligned, etc.

Python package to parse GATK Output and extract summary statistics at mbq 0,10,20,30 and variant evaluation metrics

Finds palindromes and inverted repeats in DNA Sequences based on user defined inputs

ETL scripts to populate caMOD database with MTB data from Jackson Labs

Code that polls beckman coulter and stores rack information, and protocols initiated (if any) on samples.

Takes as input FNA file, PTT file, desired probe length, cross-reactivity allowed, overhang

C++ code to calculate nmer frequencies (n= 1 to 6) and write out to file

restriction enzyme cleavage site identifier using kmp algorithm and REBASE

Converts DNA to Protein along 1, 6 (fwd or reverse strand) or user defined frames