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bioinformatics-pipeline

A pipeline bash script used for the retrieval, assembly (alignment and scaffold assembly), gene annotation, and RNA seq analysis of B. Thuringiensis sequence reads

biojava-fasta-reader

This program uses BioJava 1.7.1 packages to intake a FASTA file and parse out ORFs 1-3

dna-palindrome-generator

This program is designed to convert a DNA string into a palindrome utilizing the fewest possible nucleotide insertions - all bases from the original sequence are preserved

dna-to-amino-acid-converter

This program breaks apart a DNA string and dispalys each amino acid associated with each codon

ebola-recon

IDs Ebola positive sequence reads

fasta_parser

This program will import a fasta file, parse out the sequence ID with its associated DNA sequence, and allow the user to retrieve a DNA sequence by entering in the appropriate sequence ID

k-means-clustering-gene-expression

K-means Cluster analysis of gene expression levels provided by adrenal carcinoma cells (expression data retrieved from Bioconductor)

my-first-gui

A simple GUI I made in Java using the javax.swing library

pathogen-discovery

Analyzes long read and short-paired read data for pathogens

protein-domain-locator

This program utilizes regex patterns to locate the Zinc Finger protein domain from a FASTA file. The output will produce every Accession ID, the associated protein sequence and the Zinc FInger domain underlined in each prtoein sequence.

protein-strut-pymol

python-for-data-science-and-machine-learning

Repo of notes and projects I worked on through my Python + Machine Learning course

restriction-enzyme-recognition-site-locator

This program will read a DNA sequence from a .txt file and find each cut site and fragment length produced for a given restriction enzyme

tautyping-nf

This pipeline identifies genes or genomic segments which most closely resemble the genome-wide phylogenetic signal of a given organism using the Kendall Tau rank correlation statistic