Pinned Repositories
10genomes
These are the scripts from my phylogenetics paper. I don't think they will work as is, I just wanted to back them up. Please don't judge me for their inelegance, I made them when the only programming language I had any experience with was AWK, and not much of that.
Interactome
maize
Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
merlin-p
A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)
personal-website
Code that'll help you kickstart a personal website that showcases your work as a software developer.
SequenceClusterScripts
A set of scripts to analyze the output of a clustering program, such as orthoMCL.In their current version, most of this scripts are adapted to our local environment, and using JGI genome annotation
SingleSplice
Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: http://nar.oxfordjournals.org/content/early/2016/01/05/nar.gkv1525.full
SRW-PPINetworks
Supervised Random Walk in PPI Networks
maggishaggy's Repositories
maggishaggy/SRW-PPINetworks
Supervised Random Walk in PPI Networks
maggishaggy/merlin-p
A prior-based integrative framework for functional transcriptional regulatory network inference (Fotuhi Siahpirani & Roy, Nucleic Acids Research 2017)
maggishaggy/AGLA_GB_supp-scripts
This repository contains scripts used for various sections of the paper "Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface".
maggishaggy/Amanita_comparative_genomics
Companion scripts for Amanita comparative genomics paper "Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita"
maggishaggy/awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
maggishaggy/bibnet-google-scholar-scraper
maggishaggy/bioinfo-tools
Collection of Python and other data analysis resources
maggishaggy/bot599
Genomic Biology
maggishaggy/carveme_paper
Data and scripts for the paper "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities"
maggishaggy/CoEWC
Script for paper of a new method for the discovery of essential proteins-PLoS One 2013
maggishaggy/comparative_trypanosoma_paper
Custom scripts for recreating some of the analyses from the trypanosoma genomic comparisons work.
maggishaggy/detangle-cd
Code for Hall-Swan et al. 2017, "Detangling PPI networks to uncover functionally meaningful clusters"
maggishaggy/Drug-Resistance-Analysis-Staphylococcus-aureus
We try to find the shortest paths between the drug resistant protein interactome and the drug target proteins in Staphylococcus aureus.
maggishaggy/ggnetwork
Geoms to plot networks with ggplot2
maggishaggy/github-bioinformatics
Code for Russell et al. "A large-scale analysis of bioinformatics code on GitHub"
maggishaggy/GRFP
Here are a set of example Relevant Background and Future Goals and Graduate Research Plan Statement statements for the NSF GRFP in Ecology and Evolutionary Biology.
maggishaggy/JASPAR-UCSC-tracks
Code and data used to create custom UCSC Genome Browser tracks for JASPAR 2018.
maggishaggy/LG
maggishaggy/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
maggishaggy/network_sampling_MC
Given a protein-protein interaction network (PPIN) sample possible structures of interface interaction networks (IINs). Performs random sampling of network, and biased sampling based on the fitness function defined in Holland, D. et al., Sci. Reports, 7, 5631 (2017):https://www.nature.com/articles/s41598-017-05686-2
maggishaggy/pathways
Disease pathways in the human interactome
maggishaggy/pomegranate
Fast, flexible and easy to use probabilistic modelling in Python.
maggishaggy/PPI-Analysis
This program is intended to analyze protein interaction networks via analysis of data obtained from the PSICQUIC web app
maggishaggy/ppi-network-analysis-2
Protein-protein interaction network analysis
maggishaggy/Select_Test
maggishaggy/sendo
Scripts for the Synchytrium endobioticum genome paper
maggishaggy/SLiMEnrich
SLiMEnrich Shiny App for prediction of domain-motif interactions
maggishaggy/StableMotifs
Java library that implements the attractor finding method described in Chaos 23 (2) 025111, and the control method described in http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1004193.
maggishaggy/STRIDE
STRIDE: Species Tree Root Inference from Gene Duplication Events
maggishaggy/Ubi-prediction-SVM-project1
This project is application of machine learning in computational biology. I did most of the coding and building the front-end predictor server