A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
☆71Apr 5, 2024Updated 2 years ago
Alternatives and similar repositories for arboreto
Users that are interested in arboreto are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Scalable inference of gene regulatory networks using Apache Spark and XGBoost☆22Feb 8, 2018Updated 8 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆649Jun 26, 2025Updated last year
- ☆10Jun 13, 2025Updated last year
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆269Jan 16, 2026Updated 9 months ago
- Fast visualization tool for large-scale and high dimensional single-cell data☆80Jun 23, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ScoMAP is an R package to spatially integrate single-cell omics data into virtual cells and infer enhancer-to-gene relationships.☆30Oct 4, 2021Updated 5 years ago
- AUCell: score single cells with gene regulatory networks☆207Mar 9, 2024Updated 2 years ago
- Single Cell RNA Intron-Exon counting☆12May 7, 2020Updated 6 years ago
- ☆14Jan 23, 2025Updated last year
- Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.☆56Jun 9, 2026Updated 4 months ago
- Blood Transcription Modules for interpreting blood transcriptomics data☆11Nov 25, 2024Updated last year
- Create cisTarget databases☆65Jun 18, 2025Updated last year
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 6, 2026Updated 3 months ago
- Methods for inferring undirected networks from data☆47Mar 17, 2021Updated 5 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆185Dec 8, 2022Updated 3 years ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆88Sep 15, 2026Updated last month
- cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data☆150Apr 5, 2024Updated 2 years ago
- machine-readable file format for genomic library sequence and structure☆130Oct 25, 2026Updated last week
- Splicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data☆11Dec 11, 2025Updated 10 months ago
- Regulatory networks with Direct Information in python☆42Mar 9, 2023Updated 3 years ago
- A repository of pipelines for single-cell data in Nextflow DSL2☆81Apr 19, 2023Updated 3 years ago
- BEELINE: evaluation of algorithms for gene regulatory network inference☆220Jul 11, 2026Updated 3 months ago
- Machine learning-based approach for the inference of gene regulatory networks from expression data.☆103Sep 24, 2021Updated 5 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Finding the causality in biological pathways☆14Jul 12, 2023Updated 3 years ago
- Single cell interactive plotting tools☆25Jun 12, 2020Updated 6 years ago
- Deep learning for single-cell Gene Regulatory Networks☆15Updated this week
- ☆32May 19, 2019Updated 7 years ago
- This is the alpha version of the CellOracle package☆509Apr 30, 2026Updated 6 months ago
- Code for reproducing the Sei manuscript results☆17Jan 25, 2022Updated 4 years ago
- Python package to perform enrichment analysis from omics data.☆301Updated this week
- ☆62Mar 18, 2026Updated 7 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆501Apr 5, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Pipeline to run scE2G☆69Oct 27, 2026Updated last week
- Data-driven design of context-specific regulatory elements☆10Jun 18, 2024Updated 2 years ago
- This R package for performing module repertoire analyses and generating fingerprint representations☆19Sep 16, 2021Updated 5 years ago
- Bead-based single-cell atac processing☆33Jul 6, 2026Updated 3 months ago
- Collection of analysis methods for small count data generated by rafalab members (the methods, not the data).☆25Jul 10, 2024Updated 2 years ago
- Dorothea package in Python☆11Apr 5, 2022Updated 4 years ago
- Visualising data frames as funky heatmaps 📊, the Python implementation☆27Feb 6, 2025Updated last year