Mitchel Tumuhimbise's starred repositories
design-of-experiments
A Python Package for intuitive design of experiments with user-friendly analysis of results. The aim is for this package to rival the DOE capabilities of commercial software such as JMP. Currently designs and analysis will be more geared towards investigations following the Response Surface Methodology.
RNA-seq-analysis
RNAseq analysis notes from Ming Tang
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
DIYtranscriptomics.github.io
The website for a semester-long 'do-it-yourself' (DIY) transcriptomics course
SimpleTidy_GeneCoEx
A simple gene co-expression analyses workflow powered by tidyverse and graph analyses
BI-BE-CS-183-2023
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
bioc-intro
Bioconductor data science introduction
GS-PRACTICE
Tumor genomic subtyping tool based on mutational signautures
cancerclassifier_L
Exemplar project on how to create leukemia cancer classifier using Python and gene expression data via LGBM.
IsoformSwitchAnalyzeR
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
cshl_rstats_genome_scale_2023
CSHL Statistical Analysis of Genome Scale Data 2023
hierarchical-clustering
A Python implementation of divisive and hierarchical clustering algorithms. The algorithms were tested on the Human Gene DNA Sequence dataset and dendrograms were plotted.
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
CancerTypePrediction
This is the repository for paper titled as "Convolutional neural network models for cancer type prediction based on gene expression".
ads1-notebooks
Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing
ads1-slides
Slides for Algorithms for DNA Sequencing Coursera class
machine_learning_complete
A comprehensive machine learning repository containing 30+ notebooks on different concepts, algorithms and techniques.
mml-book.github.io
Companion webpage to the book "Mathematics For Machine Learning"
bioinf-python
Python for Bioinformatics
UCSCXenaTools
:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
MachineLearning_notes
Machine learning and deep learning resources
Cancer_notes
A continually expanding collection of cancer genomics notes and data
TCGAsurvival
Scripts to analyze TCGA data