kundajelab / ProCapNet
Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
☆13Updated 2 weeks ago
Alternatives and similar repositories for ProCapNet:
Users that are interested in ProCapNet are comparing it to the libraries listed below
- ☆26Updated last week
- Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing☆26Updated 4 months ago
- TF analysis from epigenetic and Hi-C data☆17Updated 3 weeks ago
- Code for reproducing the Sei manuscript results☆16Updated 3 years ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 3 months ago
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆31Updated 3 weeks ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆28Updated 2 weeks ago
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆14Updated 5 months ago
- ☆13Updated 4 months ago
- Use an ensemble of variant callers to call variants from ATAC-seq data☆23Updated last month
- Bioinformatic tool for Splice site Strength Estimation using RNA-seq☆15Updated this week
- Saluki, a method to predict mRNA half-lives from sequence☆24Updated 2 years ago
- Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)☆17Updated 3 years ago
- A method for analyzing scATAC-seq experiments.☆30Updated last month
- A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution☆9Updated this week
- scOpen: single-cell open chromatin analysis via NMF modelling☆26Updated 2 years ago
- Feature-rich Python implementation of the tximport package for gene count estimation.☆36Updated last month
- ☆18Updated 2 years ago
- ☆38Updated 7 months ago
- Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis☆32Updated 3 years ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆63Updated last year
- Python package to predict enhancer-gene interactions supervised on CRISPRi data☆14Updated last year
- PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data☆43Updated last year
- Benchmark of GRNs using the GRETA pipeline☆24Updated last month
- High-definition modeling of chromatin + transcriptomics data☆23Updated last week
- Toolset for training quantitative sequence to function models.☆23Updated last year
- Nextflow implementation of SpliZ☆13Updated last year
- A python package for chromVAR☆27Updated last year
- Single Cell Analysis of Five'Ends☆49Updated last year
- 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