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ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

ads1-slides

Slides for Algorithms for DNA Sequencing Coursera class

alignmentc

Alignment code in C++

batch_effects_workflow_code

Code accompanying batch effects processing workflow for "omic" data, mainly targeted for proteomics

codeshare

This repository contains code files I have been generating to learn BioInformatics

datasciencecoursera

Repository for data science course

datasharing

The Leek group guide to data sharing

deeplc

DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

dialignment

Extension of the DIAlign R package (alignment algorithm) for multi-alignment via hierarchical clustering

dialignr

This is a R package for alignment of DIA mass-spec data

easypqp

EasyPQP: Simple library generation for OpenSWATH

fit-rec

Code for WWW 19' paper

genstats

Statistics course for JHU Genomic Data Science Sequence

massformer

Tandem Mass Spectrum Prediction with Graph Transformers

mayinstitute2020-intermediater

May Institute 2020 Online - Intermediate R Crash Course

msproteomicstools

Some hopefully useful tools for mass spectrometry applied to proteomics

nn

DIA-NN - a universal automated software suite for DIA proteomics data analysis.

onlinecourses

This repo contains few courses I did to learn Bioinformatics and Machine learning

openms

The codebase of the OpenMS project

orphan-crispr-project

Python Scripts

pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.

python-cpp-challenge

A public challenge (examples and tests) for tools that provide Python interfaces to C++ libraries.

pytorch_tutorial

PyTorch Tutorial (1.3)

rptplus

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studygroup

Welcome to the University of Toronto Scientific Coders!

task208_jon

Some data from Jonathan Roth for alignment

test-repo