Aaron Odell's repositories
HiC_Genome_Assembler
Code base for a HiC based genome assembly algorithm
MLP_training_with_noisy_labels
MLP training with potentially noisy labels
SyntenicCoordinateShift
This jupyter notebook/project is essentially a set of functions that will allow for the conversion of one genomes coordinates to another via their syntenic relationship (if it exists). The program utilizes the syntenic alignment outputs from the program Satsuma (http://satsuma.sourceforge.net/) and the python intervaltree package (https://pypi.org/project/intervaltree/) to shift coordinates from one genome to another.
communityStructure_louvainMethod
This repository is a python implementation of the Lovain Method for fast unfolding of community structure in large networks (a rewording of the original paper https://arxiv.org/abs/0803.0476)
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
BamPositionalCoverageStats
This repository contains a program to query positions from an alignment file (bam file) and report back coverage statistics. Things like the number of reads found, number of As,Cs,Ts,Gs, "proper pairs", and perfect mapping quality reads.
md5SumCheck
Simple python scripts to recursively check md5sums for all files within a directory and subdirectories