Systems and Synthetic Biology's repositories
ssGSEA2.0
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
Xie_Shou_2021_SteeringEcoEvoDynamics
Source codes for "Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities"
bioscrape
BioSCRAPE (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation)
TorchProteinLibrary
PyTorch library of layers acting on protein representations
dynamo-release
Inclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
alphafold
Open source code for AlphaFold.
ModelSEEDDatabase
This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
pgap
NCBI Prokaryotic Genome Annotation Pipeline
FungalNetworkSimulations
Simulating fungal networks
NetSAM
Network Seriation And Modularization R package
MicrobeAnnotator
Pipeline for metabolic annotation of microbial genomes
gWOT
Global Waddington-OT
GNIPLR
A method of constructing regulatory network
seurat
R toolkit for single cell genomics
CellBox.jl
CellBox in Julia
azimuth
A Shiny web app for mapping datasets using Seurat v4
rEDM
Applications of Empirical Dynamic Modeling from Time Series
ipath
Metabolic pathway visualisation with iPath3 in R
CellChat
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
PROB
pseudotemporal progression-based Bayesian method for inferring GRNs from cross-sectional clinical transcriptomic data
mse_AMT
Microbial Simulation Environment - A toolbox for the simulation of genome-scale metabolic network reconstructions in the marine environment. A case study with the AMT-13 cruise transect is included.
ebdt
Python script for EBDT algorithm
scEpath
An energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data
docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics