milescsmith
Molecular biologist currently chained to a desk and mostly functioning as a code monkey. Working on precision medicine and big data with autoimmune disorders.
Oklahoma Medical Research FoundationOklahoma City, OK
Pinned Repositories
fcsjanitor
Automated cleanup of CyTOF FCS files
manifold_clustering_reduction
PLINKLiftOver
Perform liftover on plink files
pyplier
Python translation of PLIER
pysmooth
Tukey's (running median) smoother
ReducedHeat
Display gene expression along a given reduced dimension on a heatmap
ReductionWrappers
R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
scRNAimputeR
A effort to collect all of the scRNA imputation methods and allow them to interface with scRNA-seq libraries (i. e. Seurat, SingleCellAssay, etc...)
scWGCNA
Weighted gene co-expression network analysis for scRNA-seq data in Seurat
velocyto.py
RNA velocity estimation in Python
milescsmith's Repositories
milescsmith/ReductionWrappers
R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
milescsmith/PLINKLiftOver
Perform liftover on plink files
milescsmith/CITE-seq-Count
A tool that allows to get UMI counts from a single cell protein assay
milescsmith/fcsjanitor
Automated cleanup of CyTOF FCS files
milescsmith/pysmooth
Tukey's (running median) smoother
milescsmith/scvi_de
perform differential expression analysis using scVI
milescsmith/WGCNA
Updating Weighted Correlation Network Analysis
milescsmith/pyplier
Python translation of PLIER
milescsmith/velocyto.py
RNA velocity estimation in Python
milescsmith/asap_o_matic
CL python script to reformat CITEATAC fastqs for kite processing
milescsmith/cassini
ELEGOO 3D printer network protocol client
milescsmith/catch_and_kill
Simple utility to find and merge the metrics summary files from Cellranger for multiple samples
milescsmith/cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
milescsmith/control
RStudio and/or Jupyterlab-focused Docker containers for transcriptomics work
milescsmith/cytobank-uploader
A command line interface to upload FCS files to Cytobank
milescsmith/dsd
milescsmith/fingerling
Convert the binary output of Alevin into a pandas dataframe. Designed for use in ASAP-seq data analysis.
milescsmith/gtfparse
Parsing tools for GTF (gene transfer format) files
milescsmith/Microsoft-Activation-Scripts
A Windows and Office activator using HWID / Ohook / KMS38 / Online KMS activation methods, with a focus on open-source code and fewer antivirus detections.
milescsmith/new_python_module
Cookiecutter work-in-progress
milescsmith/pyalra
Python implementation of the R {ALRA} library
milescsmith/pyhsiclasso
Versatile Nonlinear Feature Selection Algorithm for High-dimensional Data
milescsmith/PyMart
Python interface towards ENSEMBL's BioMart
milescsmith/python-glmnet
A python port of the glmnet package for fitting generalized linear models via penalized maximum likelihood.
milescsmith/revseq
Simple little script to produce the reverse complement of a string
milescsmith/sc-script-gen
milescsmith/SCALEX
Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
milescsmith/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
milescsmith/scorphan
Collection of orphan utility functions for working with anndata/mudata objects
milescsmith/stl_repair
Repair STLs using Blender's "3D Print Toolbox" plugin