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aegis

Source code and documentation for AEGIS - GO analysis software

awesome-deep-learning-single-cell-papers

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

capybara

Capybara: A computational tool to measure cell identity and fate transitions

causaldiscoverytoolbox

Package for causal inference in graphs and in the pairwise settings. Tools for graph structure recovery and dependencies are included.

cellatlas

celloracle

This is the alpha version of the CellOracle package

cellot

Learning Single-Cell Perturbation Responses using Neural Optimal Transport

cinema-ot

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

crispra_zga

Code for CRISPR activation screen with single-cell RNA-seq readout studying zygotic genome activation

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.

dr-structure-preservation

A quantitative framework for evaluating data structure preservation by dimensionality reduction techniques

edge

EDGE

gears

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

geneformer

ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

giniclust2

hippo

Heterogeneity Induced Pre-Processing tOol

impa

isee

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

m-dnb-model

Identify the critical points and factors

netrex_cf

normalisr

Causal inference, differential expression, and co-expression for scRNA-seq

nvr

NVR is a python implementation of gene feature selection used in Welch et al.,2016

pando

Multiome GRN inference.

pencil

PENCIL is a novel tool for singlecell data analysis to identify phenotype associated subpopulations and informative genes simultaneously.