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2020plus

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

abm-ln-model

This is an agent-based model that illustrate the dynamics of T cell and Dendritic cell (DC) contacts time in the lymph node. This model contains two agents - T cell and dendritic cell uniformly distributed and enclosed in a cubic representation of a lymph node.

activepathways

Integrative pathway enrichment analysis of multivariate omics data

admetlab

A platform for systematic ADME evaluation of drug molecules, thereby accelerating the drug discovery process.

afm-software-list

Management of our curated AFM software list

aids-hiv_arima

R code for the ARIMA analysis of AIDS/HIV incidence and death data in China

alra

Imputation method for scRNA-seq based on low-rank approximation

am_genebasis

prediction of marker genes for cell typing and spatial gradients from scRNA-seq

amdock

(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

ampkmtor2022

anndata2ri

Convert between AnnData and SingleCellExperiment

apear

Enrichment Networks for Pathway Enrichment Analysis

asurat

ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes

atomistic.jl

Package that provides a integrated Julia workflow for molecular dyanmics simulations.

autism_precision_medicine

Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.

auto-sklearn

Automated Machine Learning with scikit-learn

autonomous-molecular-design

Sandbox for the development of active-learning algorithms for automated drug discovery.

awesome-biology

Curated (meta)list of resources for Biology.

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

awesome-multi-omics

List of software packages for multi-omics analysis

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

awesome_bigdata_ai_drugdiscovery

A collection of resources useful for leveraging big data and AI for drug discovery. It mainly serves as an orientation for new lab folks. It may be biased towards my lab interest.

awesome_spatial_omics

tools and notes for spatial omics

bayesiantools

General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

bayesspace

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

baysor

Bayesian Segmentation of Spatial Transcriptomics Data

baysoranalysis

Analysis for the Baysor paper

bi-be-cs-183-2023

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

bio331-f21

Computational Systems Biology at Reed College (Fall 2021)

bio331-utils

Utility functions for Reed College Bio331: Computational Systems Biology.