bernardo-de-almeida / DeepSTARR
Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Drosophila melanogaster S2 cells
☆56Updated last year
Alternatives and similar repositories for DeepSTARR:
Users that are interested in DeepSTARR are comparing it to the libraries listed below
- Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy☆25Updated 2 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆36Updated 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…☆31Updated this week
- https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2☆28Updated 3 weeks ago
- ☆17Updated 3 months ago
- A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence☆33Updated 9 months ago
- ExplaiNN: interpretable and transparent neural networks for genomics☆47Updated 2 weeks ago
- C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.☆69Updated 7 months ago
- code to run EPInformer for gene expression prediction and gene-enhancer links prioritization☆35Updated 2 months ago
- a toolset for mining multi-dimensional features of the translatome with ribosome profiling data☆16Updated last month
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆67Updated this week
- Saluki, a method to predict mRNA half-lives from sequence☆22Updated 2 years ago
- Computational Optimization of DNA Activity (CODA)☆55Updated last month
- HiCorr: a Hi-C data bias-correction pipeline☆28Updated last year
- Scripts + resources for analyzing combinatorial Hi-C data☆28Updated 5 years ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆27Updated this week
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆35Updated 3 weeks ago
- Single-cell Hi-C data analysis toolbox☆25Updated 3 years ago
- code to run sei and obtain sei and sequence class predictions☆97Updated 2 years ago
- ☆34Updated 2 years ago
- Estimation of Promoter Activity from RNA-Seq data☆50Updated 3 years ago
- Cooler demo using a Jupyter notebook Binder☆16Updated 4 years ago
- ☆26Updated 2 weeks ago
- Predicting gene expression levels from genomic sequences☆51Updated 4 years ago
- Bioinformatic tool for Splice site Strength Estimation using RNA-seq☆14Updated 2 years ago
- Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes☆32Updated 7 months ago
- Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing☆25Updated 2 months ago
- ☆11Updated last month
- ☆17Updated 5 months ago
- A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data☆32Updated last month