Pinned Repositories
blackjack
Blackjack simulator built in Python
cnmf
Packaged implementation of consensus nonnegative matrix factorization (cNMF; Kotliar, et al. 2019) for single-cell data analysis
furry-couscous
Tools for manipulation and analysis of single-cell and spatial transcriptomic data
kitchen
Manipulate counts matrix files and cook scRNA-seq data from command line
pga-data
Scrape PGA Tour data for historical scores and finishes
super-enhancer-testing
Testing models of super enhancers using superEnhancerModelR package from Dukler, et al. (2017)
MILWRM
Consensus tissue region identification from multiplex molecular image data for digital pathology
spatial_CRC_atlas
Code to reproduce results from Heiser, et al. (2023)
DR-structure-preservation
A quantitative framework for evaluating data structure preservation by dimensionality reduction techniques
dropkick
Automated cell filtering for single-cell RNA sequencing data
codyheiser's Repositories
codyheiser/pga-data
Scrape PGA Tour data for historical scores and finishes
codyheiser/cnmf
Packaged implementation of consensus nonnegative matrix factorization (cNMF; Kotliar, et al. 2019) for single-cell data analysis
codyheiser/furry-couscous
Tools for manipulation and analysis of single-cell and spatial transcriptomic data
codyheiser/blackjack
Blackjack simulator built in Python
codyheiser/MILWRM
Consensus tissue region identification from multiplex molecular image data for digital pathology
codyheiser/kitchen
Manipulate counts matrix files and cook scRNA-seq data from command line
codyheiser/atlasAnalysis
codyheiser/canb-ML
Supervised classification of neonatal data
codyheiser/canb-TNFa-model
Modeling TNFa - NFkB signaling after Lipniacki, et. al. (2007) using PySB
codyheiser/cfg
dotfile storage
codyheiser/cNMF_ch
Packaged consensus Non-negative Matrix Factorization for single-cell RNA-seq data
codyheiser/codyheiser.github.io
codyheiser/codypy
Useful toolkit in Python3
codyheiser/codyr
Useful toolkit in R
codyheiser/cpbp8306
Assignments for CPBP8306: Data Analysis for the Biomedical Sciences
codyheiser/dropkick-manuscript
Scripts and notebooks for reproducing analysis in the 2020 dropkick manuscript.
codyheiser/dropkick_archive
Automated cell filtering for single-cell RNA sequencing data
codyheiser/ecotyper
codyheiser/fluffy-succotash
Investigating genetic/transcriptomic/epigenetic causes of drug-induced "idling" state in BRAF melanoma
codyheiser/fuzzy-lasagna
Spatial mapping of human kidney by automated structural segmentation and registration across paired IHC, AF, and IMS datasets
codyheiser/hetio
Hetnets in Python (relocated from dhimmel/hetio)
codyheiser/imsig
Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
codyheiser/infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
codyheiser/napari-registration
A napari plugin for manual spatial registration of two images
codyheiser/pypath
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
codyheiser/pySCENIC
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
codyheiser/python-glmnet
A python port of the glmnet package for fitting generalized linear models via penalized maximum likelihood.
codyheiser/seq-tools
Basic genetic sequence processing tools
codyheiser/st_gridnet
A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.
codyheiser/tempus_tech_challenge
Bioinformatics technical challenge