EngreitzLab / CRISPR_comparison
Snakemake workflow for comparing E-G links to experimental data
☆18Updated 2 weeks ago
Alternatives and similar repositories for CRISPR_comparison:
Users that are interested in CRISPR_comparison are comparing it to the libraries listed below
- Python package to predict enhancer-gene interactions supervised on CRISPRi data☆14Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆41Updated 5 months ago
- A method for analyzing scATAC-seq experiments.☆30Updated last month
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆10Updated 5 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 3 months ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆28Updated 2 weeks ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆40Updated 3 months ago
- Code for reproducing the Sei manuscript results☆16Updated 3 years ago
- ☆25Updated last week
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆31Updated 3 weeks ago
- ☆35Updated this week
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆37Updated this week
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆20Updated last year
- Tools for sgRNA calling in direct capture Perturb-seq data☆32Updated last year
- pseudobulking on an AnnData object☆30Updated last month
- ☆35Updated 7 months ago
- High-definition modeling of chromatin + transcriptomics data☆23Updated last week
- ☆34Updated 2 years ago
- For fine-tuning Enformer using paired WGS & gene expression data☆14Updated 2 weeks ago
- PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data☆43Updated last year
- ☆17Updated 6 months ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated last year
- Using BCR and expression for sequence embedding☆21Updated 2 weeks ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆47Updated 3 weeks ago
- ACTIONet single-cell analysis framework☆38Updated 7 months ago
- Saluki, a method to predict mRNA half-lives from sequence☆24Updated 2 years ago
- Dataloader for applying sequence models to personalized genomics☆24Updated this week
- Decima is a Python library to train sequence models on single-cell RNA-seq data.☆33Updated 2 weeks ago
- ☆12Updated 2 years ago
- Mapping pipeline for snmC-seq based technologies.☆20Updated last year