Hughes-Genome-Group / deepCLinks
A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
☆33Updated last year
Alternatives and similar repositories for deepC
Users that are interested in deepC are comparing it to the libraries listed below
Sorting:
- code to run sei and obtain sei and sequence class predictions☆109Updated 2 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Updated last month
- Scripts + resources for analyzing combinatorial Hi-C data☆31Updated 6 years ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆82Updated last year
- APA Regression Net - Predict and Engineer Alternative Polyadenylation☆40Updated 4 years ago
- ☆26Updated 7 months ago
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆92Updated 9 months ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆86Updated 2 months ago
- ☆18Updated 3 years ago
- ☆69Updated 2 weeks ago
- ☆36Updated 3 years ago
- PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data☆45Updated last month
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆71Updated 2 years ago
- HiCorr: a Hi-C data bias-correction pipeline☆29Updated 8 months ago
- deep learning-inspired explainable sequence model for transcription initiation☆99Updated 9 months ago
- a toolset for mining multi-dimensional features of the translatome with ribosome profiling data☆18Updated 4 months ago
- Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellula…☆44Updated 4 years ago
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆42Updated 2 months ago
- Predicting gene expression levels from genomic sequences☆55Updated 5 years ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆29Updated 2 weeks ago
- This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge☆20Updated 5 years ago
- This repository hosts a minimal version of a Python API for BPNet.☆53Updated last month
- a computational tool for analyzing single cell Hi-C data☆26Updated last year
- Code for reproducing the Sei manuscript results☆17Updated 3 years ago
- Single-cell ATAC-seq analysis via Latent feature Extraction☆103Updated 2 years ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated last year
- A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.☆94Updated last year
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆66Updated 4 months ago
- Epimap processing and analysis code repository☆33Updated 3 years ago
- ☆32Updated 6 years ago