jzhoulab / puffin_manuscript
☆17Updated 6 months ago
Alternatives and similar repositories for puffin_manuscript:
Users that are interested in puffin_manuscript are comparing it to the libraries listed below
- ☆21Updated last year
- Bioinformatic tool for Splice site Strength Estimation using RNA-seq☆16Updated last week
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆63Updated 2 years ago
- Code for reproducing the Sei manuscript results☆16Updated 3 years ago
- Pipeline for generating reference and perturbed sequences for input into predictive models.☆10Updated 5 months ago
- Saluki, a method to predict mRNA half-lives from sequence☆24Updated 2 years ago
- ☆20Updated 2 months ago
- ☆34Updated 2 years ago
- ☆18Updated last year
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆41Updated 5 months ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment☆20Updated last year
- Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)☆17Updated 3 years ago
- PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data☆43Updated last year
- ☆18Updated 2 years ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆28Updated 3 weeks ago
- ☆10Updated 4 months ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆26Updated 2 years ago
- ☆21Updated 8 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆47Updated last month
- Dataloader for applying sequence models to personalized genomics☆25Updated this week
- ☆27Updated 3 months ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆48Updated 2 weeks ago
- A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence☆33Updated 11 months ago
- DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data☆31Updated last month
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆29Updated 3 months ago
- Snakemake workflow for comparing E-G links to experimental data☆18Updated last week
- This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge☆20Updated 4 years ago
- Computational Optimization of DNA Activity (CODA)☆56Updated last month
- For fine-tuning Enformer using paired WGS & gene expression data☆14Updated last week
- NeuronMotif: deciphering cis-regulatory codes by layerwise demixing of deep neural networks☆15Updated last year