Name: Miles Smith
Type: User
Company: Oklahoma Medical Research Foundation
Bio: Molecular biologist currently chained to a desk and mostly functioning as a code monkey.
Working on precision medicine and big data with autoimmune disorders.
Location: Oklahoma City, OK
Blog: http://www.omrf.org
Miles Smith's Projects
Isoform co-usage networks from single-cell RNA-seq data
Imputation method for scRNA-seq based on low-rank approximation
Accelerating Medicines Partnership: Rheumatoid Arthritis Phase 1
CL python script to reformat CITEATAC fastqs for kite processing
An autoencoder based imputation of the sparse single cell RNA-seq data.
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
Fork of Azimuth (Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency), updated to work with Python 3.10+
Reproducible workflows for the data analysis of "Baseline" project
Resources to learn how to use and program in R
👩🔬👨🔬 Another R Markdown Better Scientific Poster
various projects with data from boardgamegeek
A Python interface to boardgamegeek.com. Pulls information from BGG and creates Python objects for the data.
ELEGOO 3D printer network protocol client
Simple utility to find and merge the metrics summary files from Cellranger for multiple samples
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
Quickly generate SLURM job scripts for Cellranger functions. NOTE: this has been retired in favor of cellranger-scripts
Non-official Git repository for R package cellrangerRkit (currently not available elsewhere)
A tool for semi-automatic cell type classification
📜 A Cheat-Sheet Collection from the WWW
A tool that allows to get UMI counts from a single cell protein assay
CLI to apply UMAP/Leiden clustering to an array of values
Multi-condition single-cell
We wrote a getting-started file for reproducible research in computational science (computational biology).
Config files used to define parameters specific to compute environments at different Institutions
RStudio and/or Jupyterlab-focused Docker containers for transcriptomics work
Project structure for data project
A command line interface to upload FCS files to Cytobank