AquaMono's repositories
BASiCS
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
CausalDiscoveryToolbox
Package for causal inference in graphs and in the pairwise settings. Tools for graph structure recovery and dependencies are included.
CellOracle
This is the alpha version of the CellOracle package
cpa
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
crispr-bean
Bayesian Estimation of variant effect (from Base Editing reporter screens) with guide Activity Normalization
CS-CORE
R package for CS-CORE, a statistical method for cell-type-specific co-expression inference from single cell RNA-sequencing data
dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
dowhy
DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphical models and potential outcomes frameworks.
ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
Pando
Multiome GRN inference.
PENCIL
PENCIL is a novel tool for singlecell data analysis to identify phenotype associated subpopulations and informative genes simultaneously.
scDesign3
scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
scnym
Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
scPerturb
scPerturb: A resource and a python/R tool for single-cell perturbation data
SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
scran
Clone of the Bioconductor repository for the scran package.
scStateDynamics
Deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes
splatter
Simple simulation of single-cell RNA sequencing data
stable-diffusion-webui
Stable Diffusion web UI