aertslab / arboreto
A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
☆55Updated 10 months ago
Alternatives and similar repositories for arboreto:
Users that are interested in arboreto are comparing it to the libraries listed below
- Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.☆47Updated 7 months ago
- Imputation method for scRNA-seq based on low-rank approximation☆74Updated last year
- Context specific and dynamic gene regulatory network reconstruction and analysis☆113Updated 5 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆68Updated 3 weeks ago
- A repository of pipelines for single-cell data in Nextflow DSL2☆75Updated last year
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆81Updated 5 months ago
- Fast motif matching in R☆45Updated last year
- Gene regulatory network containing signed transcription factor-target gene interactions☆70Updated 9 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆59Updated last month
- R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.☆43Updated last month
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆60Updated 9 months ago
- A tool that allows to get UMI counts from a single cell protein assay☆79Updated 6 months ago
- Capybara: A computational tool to measure cell identity and fate transitions☆57Updated 2 years ago
- scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference☆38Updated 5 months ago
- Single-Cell Clustering Assessment Framework☆99Updated last year
- R script for the covid balf data analysis☆65Updated 4 years ago
- ☆34Updated 9 months ago
- Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"☆53Updated 4 years ago
- This contains the dataset for comparing scRNA-seq analysis methods☆90Updated 4 years ago
- Identifying tumor cells at the single-cell level using machine learning☆48Updated 3 months ago
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆41Updated last year
- Geometry-preserving random sampling☆78Updated 3 months ago
- scWGCNA☆56Updated 2 years ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…☆60Updated 4 months ago
- ☆46Updated 2 years ago
- ☆57Updated 5 months ago
- SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.☆72Updated 9 months ago
- Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…☆40Updated 2 years ago
- pseudobulking on an AnnData object☆28Updated last year