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/Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
maggishaggy/personal-website
Code that'll help you kickstart a personal website that showcases your work as a software developer.
maggishaggy/academicpages.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
maggishaggy/amp_phase1_ra
Use single-cell transcriptomics and proteomics to study autoimmune diseases (AMP Phase I paper)
maggishaggy/appinetwork
construction and Analysis of Protein-Protein Interactions (PPI) NETWORKS for complexes and biological processes
maggishaggy/aspergillus_ps
In this repository I describe the workflow followed to process and analyze the data of the study "A genomic view on Aspergillus fumigatus against 18 species of the genus Aspergillus: Conservation, evolution and specific virulence genes"
maggishaggy/beautiful-jekyll
:sparkles: Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll
maggishaggy/C2
an approval process automation tool
maggishaggy/cbioportal
cBioPortal for Cancer Genomics
maggishaggy/ComparativeGenomics
A pipeline for processing data in a comparative genomics project.
maggishaggy/ComputationalGenomicsManual
Robs manual for the computational genomics and bioinformatics class.
maggishaggy/DeepFE-PPI
maggishaggy/EdwardsLab
Code from the Edwards lab, including bioinformatics, image analysis and more. All this code is created and maintained by folks at Rob Edwards' bioinformatics lab at SDSU.
maggishaggy/ensembl-compara
The Ensembl Compara Perl API and SQL schema
maggishaggy/familyanalyzer-deprecated
maggishaggy/fastq-pair
Match up paired end fastq files quickly and efficiently.
maggishaggy/iHam
Widget to visualise the evolutionary history of gene families
maggishaggy/machine-learning-resource
maggishaggy/OmicsIntegrator2
Prize-Collecting Steiner Forests for Interactomes
maggishaggy/PCSF
maggishaggy/pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
maggishaggy/RACA
maggishaggy/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
maggishaggy/scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
maggishaggy/scVI
Deep generative modeling for single-cell transcriptomics
maggishaggy/seurat
R toolkit for single cell genomics
maggishaggy/sjackman.github.io
The personal web site of Shaun Jackman
maggishaggy/snakemake-rnaseq
RNA-seq workflow for Snakemake based on STAR and featureCounts.
maggishaggy/statements
Successful Job Applications and Grants
maggishaggy/website
my website's jekyll code