Pinned Repositories
2020-08-17-ucmerced
Carpentry workshop for GROW
2022-06-06-JGI-UCM
In collaboration with the Black Women in Computational Biology, I led this 1-day hands-on training workshop to teach learners the fundamentals of bash command-line for file system navigation and data wrangling of common genomics flat test files
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.
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.
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
tRNA_introns
rhondene's Repositories
rhondene/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.
rhondene/Codon-Usage-in-Python
Python3 implementation of commonly used codon usage statistics
rhondene/Codon2Vec
Neural network based tool for predicting expression ('high' or 'low') directly from protein-coding sequences.
rhondene/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
rhondene/tRNA_introns
rhondene/2020-08-17-ucmerced
Carpentry workshop for GROW
rhondene/2022-06-06-JGI-UCM
In collaboration with the Black Women in Computational Biology, I led this 1-day hands-on training workshop to teach learners the fundamentals of bash command-line for file system navigation and data wrangling of common genomics flat test files
rhondene/Adaptive_Codon_Usage_Kingdom_Fungi
rhondene/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
rhondene/Deep_Learning.ai
Repository of my programming assignments from the Deep Learning.ai specialization course taught by the Dr. Andrew Ng. Python with Keras
rhondene/DATA_SCIENCE_IN_BIOLOGY
projects using galaxy, python, linux command line to analyze sequencing data
rhondene/Data_Structures-Algortihms
Python3 code for popular data structures and algorithms. Helpful for coding interviews
rhondene/deep-learning-book
Repository for "Introduction to Artificial Neural Networks and Deep Learning: A Practical Guide with Applications in Python"
rhondene/fast_template
A template for really easy blogging with GitHub Pages
rhondene/Genomics_code
an assortment of code I wrote for various genomics related tasks
rhondene/github-slideshow
A robot powered training repository :robot:
rhondene/guacomole1
data carpentry example
rhondene/In-depth-NGS-Data-Analysis-Course
Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.
rhondene/kadambari
A collection of scripts.
rhondene/Machine-Learning---Python
Popular Supervised/Unsupervised and ANN in Python. Updating....
rhondene/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.
rhondene/msu_ngs2015
DE analysis module for Week3
rhondene/OpenRefine
OpenRefine is a free, open source power tool for working with messy data and improving it
rhondene/population_genetics_Python
Python code for analysis of the 1000Genomes dataset in fulfillment of my graduate level Biostatistics course.
rhondene/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 ;)
rhondene/Probablistic_Bayesian_Models
Probabilistic programming based on Bayesian Inference Python (PyMC3). One of my computational learning goals is probablistic machine learning.
rhondene/python-novice-inflammation
Software Carpentry introduction to Python for novices using inflammation data.
rhondene/Pytorch_Practice
Notebooks curating my journey of learning pytorch
rhondene/rhondenewint
my personal academic website
rhondene/wishbone
Wishbone is an algorithm to align cells along developmental trajectories with branches