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bds-files

Supplementary files for my book, "Bioinformatics Data Skills"

bioinformatics_using_python

This repository is for all the different function commonly used for bioinformaticians to evaluate Genetic Data

biopython

Official git repository for Biopython (originally converted from CVS)

cleaning_manipulating_data

In this repository is dedicated to small projects whose focus is on practicing cleaning, analyzing, and debugging large data.

coursera_training

Linear Regression is when you have a group of points on a graph, and you find a line that approximately resembles that group of points. A good Linear Regression algorithm minimizes the error_, or the distance from each point to the line. A line with the least error is the line that fits the data the best. We call this a line of _best fit.

dlab_visualization_with_python

Material for the D-Lab's visualization workshop

final-nn-cb

Implement a generic neural network class and use it for autoencoding and classifying.

hello-world

My first project using Github

hw1_fast_aq-parse_cb

Building a FAST[AQ] Parser + Building a DNA -> RNA Transcriber

hw2-bfs_cb

HW2 BFS

hw3-clustering_cb

hw4-prim-mst_cb

Implement Prim's algorithm to construct a minimum spanning tree.

hw5-nw-cb

Project 5: Needleman-Wunsch Global Alignment

hw6-hmm-viterbi-cb

Implementation of the Viterbi algorithm, a dynamic program that is a common decoder for Hidden Markov Models (HMMs).

hw7-regression-cb

Implement a logistic regression classifier using gradient descent.

intro_to_machine_learning_with_python

monte_carlo_statistics

How to estimate a value of Pi using the Monte Carlo Method - generate a large number of random points and see how many fall in the circle enclosed by the unit square.

protein_alphafold

Different Jupyter Notebooks and available resources beneficial for proteomic analysis.

scatac-seq_hematopoietic

summer_internship_2020

In this study, we will analyze the gene expression differnt coronaviruses (CoVs) infections to determine how each virus differs when causing a disease. Here, we focuses the analysis on samples from SARS-CoV-1, MERS, and SARS-CoV-2. The raw sequence data (fastq files) for the SARS-CoV-1 and MERS infections were downloaded from GEO [GSE56192](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56192), including their corresponding Mock-treated controls). The raw sequence data (fastq files) for the SARS-CoV-2 infections were downloaded from GEO ([GSE147507](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147507)), including their corresponding Mock-treated controls). In this Jupyter notebook, I will use both R and Python to analyze three viruses: MERS, SARS-CoV-1, amd SARS-CoV-2

temperature_convertor

Description: Temperature Convertor, inputs Kelvin, Celsius, or Fahrenheit and converts to desire temperature"""

workshops_uw_seattle

xenofilter

Filtering of PDX samples for mouse derived reads