Pinned Repositories
16s-rRNA-Sanger
Snakemake pipeline for paired-end sanger sequences of 16s rRNA
Annotating_from_PDB
Annotates sequences with Eggnog-mapper and hhblits against PDB70
Applied-Bioinformatics
Student course material for the Applied Bioinformatics course at Scripps Research
ipynb_and_notes
viajes_chile
matrs's Repositories
matrs/16s-rRNA-Sanger
Snakemake pipeline for paired-end sanger sequences of 16s rRNA
matrs/Applied-Bioinformatics
Student course material for the Applied Bioinformatics course at Scripps Research
matrs/ipynb_and_notes
matrs/431notes-2017
Data Science for Biological, Medical and Health Research: Notes for 431
matrs/Applied_Machine_Learning
This repository contains my solutions for assignments given in class for COMS W4995 Applied Machine Learning Spring 2020
matrs/assembly-illumina-bact
Assembling short genomic reads from bacteria
matrs/BBMap
(Not Offical) BBMap short read aligner, and other bioinformatic tools.
matrs/BE_ISS_pangenomes
Data repo for our publication, "Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil. mSystems 4:e00281-18."
matrs/comm_genomes
matrs/crc_meta
Code and analysis results for the CRC shotgun meta-analysis
matrs/data-driven-web-apps-with-flask
Course demo code and other hand-out materials for our data driven web apps in Flask course
matrs/datastructures
misc materials for the data structures course
matrs/dotfiles
netj's dotfiles
matrs/elegant-scipy
1st Edition of Elegant SciPy (O'Reilly Publishers)
matrs/genome-sketching
online notebooks for a review of genome sketching
matrs/intro-bioinformatics
Website and slides for intro to bioinformatics class at Fred Hutch
matrs/jupytext
Jupyter notebooks as Markdown documents, Julia, Python or R scripts
matrs/microbe-dbs
:microscope: microbes-dbs utilities to fetch microbe relevant databases
matrs/numerical-python
Source code for 'Numerical Python' by Robert Johansson
matrs/PEPPAN
Phylogeny Enhanded Prediction of PAN-genome
matrs/Quality_control
Snakemake pipeline for quality control using Fastqc and Fastq Screen
matrs/R-microbial-genomics
matrs/responsive-nav.js
Responsive navigation plugin without library dependencies and with fast touch screen support.
matrs/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
matrs/rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
matrs/snakemake-wrappers
:snake: Snakemake wrappers for bioinformatics.
matrs/Statistical-Rethinking
An interactive online reading of McElreath's Statistical Rethinking
matrs/statistical-rethinking-1
Solutions for the practice problems
matrs/statsintro_python
Python modules and IPython Notebooks, for the book "Introduction to Statistics With Python"
matrs/talking-between-python-and-js
Talking to Python from JavaScript (and Back Again!)