aertslab / CREstedLinks
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
☆56Updated last week
Alternatives and similar repositories for CREsted
Users that are interested in CREsted are comparing it to the libraries listed below
Sorting:
- A method for analyzing scATAC-seq experiments.☆34Updated 6 months ago
- Pipeline to run scE2G☆32Updated 2 months ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆126Updated last month
- Geometry-preserving random sampling☆95Updated last year
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆79Updated 3 weeks ago
- Benchmark of GRNs using the GRETA pipeline☆30Updated last week
- ☆57Updated last month
- ☆37Updated last year
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆44Updated last month
- Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.☆33Updated last month
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆57Updated last year
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆67Updated 6 months ago
- ☆35Updated 10 months ago
- Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.☆54Updated last year
- Multi-omic velocity inference☆113Updated last year
- Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets☆42Updated 5 months ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Updated last year
- A python package for chromVAR☆32Updated 2 years ago
- Functional Inference of Gene Regulation☆49Updated last year
- Gene regulatory network containing signed transcription factor-target gene interactions☆94Updated 7 months ago
- Clonotype Neighbor Graph Analysis☆93Updated 4 months ago
- BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data☆29Updated last year
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆56Updated 7 months ago
- This repository hosts a minimal version of a Python API for BPNet.☆53Updated 2 months ago
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆59Updated 3 weeks ago
- pseudobulking on an AnnData object☆34Updated 10 months ago
- Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA☆82Updated 8 months ago
- Single cell omics biology annotations☆51Updated 8 months ago
- ☆26Updated 9 months ago
- Gene regulatory network inference for RNA velocity and pseudotime data☆27Updated 2 months ago