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☆110Updated 3 years ago
- ☆18Updated 3 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph☆92Updated 2 months ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆82Updated last year
- Predicting gene expression levels from genomic sequences☆54Updated 5 years ago
- HiCorr: a Hi-C data bias-correction pipeline☆30Updated 9 months ago
- PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data☆45Updated 3 months ago
- ☆26Updated 8 months ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆30Updated last month
- model-based understanding of single-cell CRISPR screening☆26Updated last year
- ☆36Updated 3 years ago
- ☆69Updated last month
- sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale☆92Updated 10 months ago
- a computational tool for analyzing single cell Hi-C data☆26Updated last year
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆11Updated last year
- APA Regression Net - Predict and Engineer Alternative Polyadenylation☆40Updated 4 years ago
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆71Updated 2 years ago
- Scripts + resources for analyzing combinatorial Hi-C data☆31Updated 6 years ago
- deep learning-inspired explainable sequence model for transcription initiation☆100Updated 10 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆49Updated 9 months ago
- Code for reproducing the Sei manuscript results☆17Updated 3 years 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
- ☆22Updated 8 years ago
- Saluki, a method to predict mRNA half-lives from sequence☆27Updated 3 years ago
- code to run EPInformer for gene expression prediction and gene-enhancer link prediction☆44Updated 3 months ago
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆32Updated 11 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
- a toolset for mining multi-dimensional features of the translatome with ribosome profiling data☆18Updated 5 months ago
- Deep Learning Method to Identify Cancer Associated TCRs☆46Updated 3 years ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆90Updated 2 months ago