noahaus

bacteria_SNP

Salvador Lab in-house variant calling script for Sapelo2 (still in development )

dev_script

Cluster scripts and programs

Micellaneous-Tools

Programs that push me to understand the python programming language.

NAST

pairwise BLAST, but with a hint of Noah

noahaus.github.io

pansplit

a command line tool for pangenome creation based on metadata

recombination_heatmap

takes the gubbins GFF output and creates a heatmap csv for further processing

sapientbio_project

sliding-window-scripts

python scripts to analyze multi-sequence alignment (FASTA) data

mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.

noahaus/dev_script

Cluster scripts and programs

noahaus/bacteria_SNP

Salvador Lab in-house variant calling script for Sapelo2 (still in development )

noahaus/sliding-window-scripts

python scripts to analyze multi-sequence alignment (FASTA) data

noahaus/ai-hackathon-flask

noahaus/ANOMA

an R command line tool to find outliers in data unsupervised

noahaus/CPPHelloWorld

Code for C++ beginner

noahaus/EpiModel

Mathematical Modeling of Infectious Disease Dynamics

noahaus/METRI

Multiomic integration of metagenomic and metatranscriptomic data

noahaus/MLMessage

Web App Messaging with Machine Learning features built in place

noahaus/NAST

pairwise BLAST, but with a hint of Noah

noahaus/noahaus.github.io

noahaus/pansplit

a command line tool for pangenome creation based on metadata

noahaus/recombination_heatmap

takes the gubbins GFF output and creates a heatmap csv for further processing

noahaus/sapientbio_project

noahaus/mbovpan_auxilary_files

files that assisted in development of mbovpan, but are not necessarily needed in the main repo

noahaus/Mod5_ECOL8540

noahaus/MSA_trim

A tool to trim multi-sequence alignment for gaps and ambiguity codes.

noahaus/multihostR

Transmission Simulator based on Multi-Host SIR model parameters.

noahaus/PangenomePipelineScripts

A repository for the scripts I developed to do pangenome inference using SPAdes, prokka, and Roary.

noahaus/Presentations

All my presentations through the PhD process

noahaus/Scoary

Pan-genome wide association studies

noahaus/SNP-Align

take VCF files (preferably filtered) and creates fasta output for SNP positions.

noahaus/SRA_scraper

A tool to access NCBI SRA Run Selector metadata

noahaus/SupervisedMotifScanner

Generate a PSSM with sequence test data. non concurrent

noahaus/TRP-orfamide-interaction

in-silico modeling of TRP28 protein for docking analysis of orfamide A, a toxin of microalgae C. reinhardtii

noahaus/vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

noahaus/VCF_parser

extract no. of SNP, Insertions, and Deletions

noahaus/vSNP

vSNP -- bacterial validation SNP analysis tool -- USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. SNP pipeline. Genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees.

noahaus/vSNP_filter

bash script to filter out poor mapping quality SNPs called from vSNP program and PE/PPE genes from analysis.

noahaus/website

Nextflow public web site