codyheiser Goto Github PK

atlasanalysis

blackjack

Blackjack simulator built in Python

canb-ml

Supervised classification of neonatal data

canb-tnfa-model

Modeling TNFa - NFkB signaling after Lipniacki, et. al. (2007) using PySB

cfg

dotfile storage

ch_utils

Storage of general utility files for shell configuration, etc.

clip-on

Kicking around Tuxedo suite for RNA-seq analysis

cnmf

Packaged implementation of consensus nonnegative matrix factorization (cNMF; Kotliar, et al. 2019) for single-cell data analysis

cnmf_ch

Packaged consensus Non-negative Matrix Factorization for single-cell RNA-seq data

codyheiser.github.io

codypy

Useful toolkit in Python3

codyr

Useful toolkit in R

cpbp8306

Assignments for CPBP8306: Data Analysis for the Biomedical Sciences

dropkick-manuscript

Scripts and notebooks for reproducing analysis in the 2020 dropkick manuscript.

dropkick_archive

Automated cell filtering for single-cell RNA sequencing data

ecotyper

fluffy-succotash

Investigating genetic/transcriptomic/epigenetic causes of drug-induced "idling" state in BRAF melanoma

furry-couscous

Tools for manipulation and analysis of single-cell and spatial transcriptomic data

fuzzy-lasagna

Spatial mapping of human kidney by automated structural segmentation and registration across paired IHC, AF, and IMS datasets

hetio

Hetnets in Python (relocated from dhimmel/hetio)

imsig

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

jukebox

Collaborative Spotify listening experience

kitchen

Manipulate counts matrix files and cook scRNA-seq data from command line

milwrm

Consensus tissue region identification from multiplex molecular image data for digital pathology

napari-registration

A napari plugin for manual spatial registration of two images

pga-data

Scrape PGA Tour data for historical scores and finishes

pypath

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.

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.

python-glmnet

A python port of the glmnet package for fitting generalized linear models via penalized maximum likelihood.