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applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

cornell-cs5785-applied-ml

Teaching materials for the applied machine learning course at Cornell Tech

crisprseq

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

csx46

Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University

distance_hinge_residue

drugz

DRUGZ software

ffq

A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA.

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

homemade-machine-learning

🤖 Python examples of popular machine learning algorithms with interactive Jupyter demos and math being explained

ibm3202

Google Colab Tutorials for IBM3202

illustrated-machine-learning.github.io

Website containing illustrations about Machine Learning theory!

localpdb

Python package to manage protein structures and their annotations

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

mit-15-003-data-science-tools

Study guides for MIT's 15.003 Data Science Tools

molmin

Macro-Molecule mutater and minimizer

multi-package-containers

Testing building mulled containers for multi-requirement tools.

obtain-chromosomal-position-from-rsid

This is a R script of getting chromosomal positions of the individual variants from rs id list

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

pdbe-api-training

Interactive Python notebooks for PDBe API training

pdbfinder

a collection of scripts and files to help in PDB retrieval for various projects

pdbrenum

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.

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

tutorials

Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.

variant2pdb

Variant mappinng on PDB structures