YogiOnBioinformatics
Aspiring Scientist, Author, Philosopher. Computational Biology PhD Student @ UVA Medicine
University of Virginia (UVA) MedicineCharlottesville, VA
Pinned Repositories
Algorithm-Implementation
Projects and Essays from Algorithm Implementation (CS 1501) at University of Pittsburgh
Assorted-Computational-Genomics-Data-Visualizations
Biplots, Volcano plots, PCA plots, Heatmaps and more Computational Genomics data created and visualized during University of Pittsburgh course, Computational Biology (BIOSC1540), with Dr. Miler Lee
Computational-Drug-Discovery-Internship-at-Merck
Description of work done at Merck pharmaceutical company in the summer of 2018 as a Computational Drug Discovery Intern at West Point, PA. Information excludes all proprietary information belonging to Merck & Co.
Differential-Gene-Expression-Analysis-with-Machine-Learning-Using-Dexamethasone-Treatment-Data
Worked with fellow peers at University of Pittsburgh under supervision of Dr. Junshu Bao, Department of Statistics, University of Pittsburgh, to do a Differential Gene Expression Analysis on a Dexamethasone treatment data set and incorporated Machine Learning into project.
Hidden-Markov-Model-based-Integration-of-Multi-Assay-Epigenomics-Samples
Integration of ATAC-Seq and multi-assay ChIP-Seq data using IDEAS (Hidden Markov Model) approach.Multi-Epigenomic state annotation with CHDI NeuroLINCS Epigenomics data using the tool "IDEAS"
Maternal-to-Zygotic-Transition-in-Xenopus-laevis
Research project undertaken in Computational Genomics at the University of Pittsburgh. with Dr. Miler Lee and students to understand Maternal-to-Zygotic transition in Xenopus laevis
ProteinVR
Protein Virtual Reality is a University of Pittsburgh project with Dr. Jacob D. Durrant that is the world's first anatomical and protein visualization VR program tailored for collegiate-biology courses.
Synthetic-Biology
Presentations and work done for University of Pittsburgh course, Synthetic Biology.
Teaching-Assistant-Computational-Genomics
Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.
Tumor-Exome-Mutation-Analysis
Statistical analysis on Mutation Annotation Format files from Whole-Exome Sequencing of Tumor samples and Controls.
YogiOnBioinformatics's Repositories
YogiOnBioinformatics/ProteinVR
Protein Virtual Reality is a University of Pittsburgh project with Dr. Jacob D. Durrant that is the world's first anatomical and protein visualization VR program tailored for collegiate-biology courses.
YogiOnBioinformatics/Computational-Drug-Discovery-Internship-at-Merck
Description of work done at Merck pharmaceutical company in the summer of 2018 as a Computational Drug Discovery Intern at West Point, PA. Information excludes all proprietary information belonging to Merck & Co.
YogiOnBioinformatics/Differential-Gene-Expression-Analysis-with-Machine-Learning-Using-Dexamethasone-Treatment-Data
Worked with fellow peers at University of Pittsburgh under supervision of Dr. Junshu Bao, Department of Statistics, University of Pittsburgh, to do a Differential Gene Expression Analysis on a Dexamethasone treatment data set and incorporated Machine Learning into project.
YogiOnBioinformatics/Synthetic-Biology
Presentations and work done for University of Pittsburgh course, Synthetic Biology.
YogiOnBioinformatics/Hidden-Markov-Model-based-Integration-of-Multi-Assay-Epigenomics-Samples
Integration of ATAC-Seq and multi-assay ChIP-Seq data using IDEAS (Hidden Markov Model) approach.Multi-Epigenomic state annotation with CHDI NeuroLINCS Epigenomics data using the tool "IDEAS"
YogiOnBioinformatics/Joint-Genotyping-2021-2022
Joint Genotyping in MIT Fraenkel Lab with ALS Genomics + 1000 Genomes Data
YogiOnBioinformatics/Maternal-to-Zygotic-Transition-in-Xenopus-laevis
Research project undertaken in Computational Genomics at the University of Pittsburgh. with Dr. Miler Lee and students to understand Maternal-to-Zygotic transition in Xenopus laevis
YogiOnBioinformatics/Teaching-Assistant-Computational-Genomics
Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.
YogiOnBioinformatics/Tumor-Exome-Mutation-Analysis
Statistical analysis on Mutation Annotation Format files from Whole-Exome Sequencing of Tumor samples and Controls.
YogiOnBioinformatics/AALS-Epigenomics-Signal-Reproducibility
Determining reproducibility of Epigenomic signal for Answer ALS
YogiOnBioinformatics/Applied-Linear-Algebra-MATH-3350
Handwritten work & R code related to University of Virginia's MATH 3350 ( Applied Linear Algebra)
YogiOnBioinformatics/B-Cells-In-Atherosclerosis
Work done during rotation with Coleen McNamara & Stefan Bekiranov in UVA BIMS PhD program
YogiOnBioinformatics/Bioinformatics-for-Protein-Ligand-Interactions
Published work of mine in Pitt Biological Sciences Advising Blog about using Bioinformatics to predict Ligand-Protein interactions.
YogiOnBioinformatics/BLAST-Biopython-Challenge
Challenge to efficiently BLAST files (FASTA file & quality scores) and report key metrics about FASTA back to user.
YogiOnBioinformatics/ChemInformatics-Machine-Learning-with-NNScore-2.0
Project in the Durrant Lab at UPitt that wanted to re-use code from a previous neural network ligand-protein interaction software to extract features for ML
YogiOnBioinformatics/ChIP-Seq-Analysis-Nanog-and-H3K27Ac
Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.
YogiOnBioinformatics/Comp-Bio-Images
Containers that I use in my work.
YogiOnBioinformatics/Computational-Biology-Research-Assistant
Links to other repositories containing all the work I did as a Computational Biology Research Assistant in the Dr. Jacob D. Durrant Lab of Computational Drug Discovery, University of Pittsburgh.
YogiOnBioinformatics/COPD-Clinical-Metric-Prediction-from-RNA-Seq
Work done during rotation with Ani Manichaikul during UVA PhD program
YogiOnBioinformatics/DAME-Destruction-of-Aqueous-Microfibers-Enzymatically
Destruction of Aqueous Microfibers Enzymatically (DAME): A novel Synthetic Biology systems approach to destroying Polyester-based Microplastic fibers
YogiOnBioinformatics/Data-Structure-Implementations
A repository containing examples of Data Structure Implementations that I did during my University of Pittsburgh course CS445: Data Structures-Abstractions and Implementations
YogiOnBioinformatics/dotfiles
Dotfiles + config files that I use in my personal and professional work.
YogiOnBioinformatics/Epigenomics-of-Novel-iPSC-derived-ALS-Cortical-Neurons
Validating the first human iPSC-derived Cortical Neuron ALS model via systematic Epigenomic analysis.
YogiOnBioinformatics/Multi-Epigenomics-ElasticNet-Ordinal-Regression
Ordinal Logistic Regression with ElasticNet Regularization using Multi-Assay Epigenomics Data from CHDI NeuroLINCS Consortium.
YogiOnBioinformatics/resource-files
Common resource files necessary for Computational Biology research.
YogiOnBioinformatics/Six-Degrees-of-Hollywood
Web game inspired by Six Degrees of Kevin Bacon, a game based on the theory of six degrees of separation. The idea of six degrees of separation suggests that any given person is only six or fewer social connections away from any other person. Our game challenges the player to link a starting actor to a goal actor using movie appearances and fellow cast members.
YogiOnBioinformatics/skills-code-with-codespaces
An exercise in using GitHub's Codespaces
YogiOnBioinformatics/skills-hello-github-actions
My clone repository
YogiOnBioinformatics/Teaching-Assistant-Computational-Structural-Biology
Course schedule from experience as a selected Undergraduate Teaching Assistant at the University of Pittsburgh course, BIOSC 1540 - Computational Structural Biology, taught by Dr. Jacob Durrant.
YogiOnBioinformatics/YogiOnBioinformatics
Get to know more about YogiOnBioinformatics (Yogindra Raghav), Bioinformatics scientist at MIT and the Broad Institute of MIT and Harvard.