rhondene Goto Github PK

2020-08-17-ucmerced

Carpentry workshop for GROW

2022-06-06-jgi-ucm

I co-organized this 1-week hands-on training workshop to teach learners the fundamentals of programming and data science that are essential to get started on data-driven research projects.

adaptive_codon_usage_kingdom_fungi

ads1-notebooks

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

analyzing-sequencing-dna-reads

Python implementation of biosequence analysis algorithms I learnt in the amazing online course Algorithms for DNA Sequencing by John's Hopkin via Coursera

codon-usage-in-python

Python3 implementation of commonly used codon usage statistics

codon2vec

Neural network based tool for predicting expression ('high' or 'low') directly from protein-coding sequences.

compgenr

data_science_in_biology

projects using galaxy, python, linux command line to analyze sequencing data

data_science_ml_lessons_biology

Tutorials on data science/machine learning using Python with a life-science perspective. When I started learning programming and machine learning, most of the examples were from other fields like IT or business, so sometimes I found it difficult to apply those skills to biological problems. I help make data science and machine learning more relatable and practical to beginners, especially in my major biology by sharing the skills and knowledge I have acquired in data science and computation. I will do my best to use biological datasets as examples.

data_structures-algortihms

Python3 code for popular data structures and algorithms. Helpful for coding interviews

deep-learning-book

Repository for "Introduction to Artificial Neural Networks and Deep Learning: A Practical Guide with Applications in Python"

deep_learning.ai

Repository of my programming assignments from the Deep Learning.ai specialization course taught by the Dr. Andrew Ng. Python with Keras

fast_template

A template for really easy blogging with GitHub Pages

genomics_code

an assortment of code I wrote for various genomics related tasks

github-slideshow

A robot powered training repository :robot:

guacomole1

data carpentry example

in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

kadambari

A collection of scripts.

machine-learning---python

Popular Supervised/Unsupervised and ANN in Python. Updating....

machine-learning-octave

Matlab/Octave implementation of supervised and unsupervised machine learning algorithms I learnt from the popular online course Machine Learning taught by Dr. Andrew Ng.

misc_bioinformatics

Stores scripts I commonly use during bioinformatic analysis so I don't have to dig through old code. I work primarily with Drosophila (Flybase) annotation files

msu_ngs2015

DE analysis module for Week3

openrefine

OpenRefine is a free, open source power tool for working with messy data and improving it

population_genetics_python

Python code for analysis of the 1000Genomes dataset in fulfillment of my graduate level Biostatistics course.

probabilistic-programming-and-bayesian-methods-for-hackers

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

probablistic_bayesian_models

Probabilistic programming based on Bayesian Inference Python (PyMC3). One of my computational learning goals is probablistic machine learning.

python-novice-inflammation

Software Carpentry introduction to Python for novices using inflammation data.

pytorch_practice

Notebooks curating my journey of learning pytorch

rhondenewint

my personal academic website