Evan Peikon

Bioinformatics_Toolkit. A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

math_for_compbio. This repository contains math tutorials I created for Bioinformatics and Computational Biology.

bash_fundamentals. Introduction to Bash for bioinformatics

Python_Fundamentals_Biology. Python Fundamentals for Biologists

scRNA-seq-guide. A DIY Guide To Single-Cell RNA-Sequencing Analysis

R_Fundamentals_Biologists. R Fundamentals for Biologists

Build_A_Biomarker. A DIY Guide to Developing Proteomic Biomarker Panels

systems_biology. Assorted functions for performing numerical methods and solving common problems in systems biology

PPI_Network_Analysis. Mapping DEGs to PPI Networks, Identifying Network Hubs and Highly Connected Proteins, and Simulating Genetic Circuits. An End-to-End DIY Guide

Amilioride_Drug_MOA. Uncovering Amiloride's Mechanisms of Action in Multiple Myeloma: A Bioinformatics Approach

functional_enrichment_analysis. A DIY guide to gene ontology, pathway, and gene set enrichment analysis

Evaluating_ML_Biology. A biotechnologist's guide to evaluating machine learning algorithms, with practical Python examples

SmallSeqFlow. SmallSeqFlow: A streamlined, notebook-based bulk RNA-seq analysis pipeline optimized for small-sample studies with modular extensions.

PhysioNexus. PhysioNexus is a open source tool that transforms complex time series data into intuitive network visualizations showing cause-and-effect relationships between physiological data, environmental variables, and external load measurements.

BLAST. A DIY Guide To BLAST Tools For Sequence Alignment

co_expression_network. A DIY guide to gene co-expression network analysis

Machine-Learning. Assorted ML tutorials that I originally wrote for Decoding Biology

Mouse_Alz_Models. Exploring mutual features between the 5xFAD, 3xTG-AD, and PS3O1S Alzheimer's Disease Mouse Models

scRNA_Prediction. Predictive Modeling of Gene Expression in Skeletal Muscle Using scRNA-seq

biophysics_expert. BiophysicsExpert is an educational tool that provides users with a searchable database of over 150 biophysics formulas, allowing them to quickly find equations based on known variables or desired unknowns.

viral-proteome. Decoding the herpes virus proteome and analyzing amino acid frequencies to uncover potential drug targets

scRNA-Seq-ScanPy. Identifying and visualizing marker genes with Scanpy

GSE_130646. Analysis of single-cell transcriptional profiles in human skeletal muscle

data_science_at_the_command_line. Notes from "Data Science at the Command Line" by Jeron Janssens

dynamicalsys. An introduction to dynamical systems and markov models

CausalEdge. A Granger Causality and Mediation Framework for Inferring Direct Causal Networks in Time-Series Proteomics

CompBio_Coding_Challenge. Assorted coding challenges

Temporal_Transcriptomic_3xTG-AD. Temporal Transcriptomic Analysis of Alzheimer's Disease Progression in 3xTg-AD Mice

GSE118523. Analysis from CNS cell-type specific gene profiling of aging P301S tau transgenic mice

codon-freq. Find codon frequency and usage bias

Modeling_time_to_exhaustion. Modeling time-to-exhaustion using the critical power / W' balance and critical metabolic rate / M' balance models.

GSM_6611295. Replicating analyses from Lovric et al's 2023 paper "Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle"

23andMe. Analyzing raw data from 23andMe

intensity_prediction. Predicting exercise intensity zones using an unsupervised learning model with using muscle oxygenation data and its derivatives.

Decoding_Biology. Code from Decoding Biology Articles / shorts

GVA-analysis. DIY guide to genomic variant analysis

evanpeikon. Config files for my GitHub profile.

SmallSeqFlow_SnakeMake. Python

Wearable_DataScience. An in-depth guide to sliding window methods and two-pointer techniques for analyzing time-series physiological data

Decypher. Decypher analyzes time-series biomarker, behavioral, environmental, and health data to map causal pathways driving health outcomes and identify high-leverage intervention targets.