Alternatives and similar repositories for DeepSTARR

Users that are interested in DeepSTARR are comparing it to the libraries listed below

• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 6 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 11 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆80Updated last year
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 9 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 7 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated last month
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆93Updated 7 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆52Updated this week
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆70Updated 10 months ago
• vagarwal87 / saluki_paper
  Saluki, a method to predict mRNA half-lives from sequence
  ☆25Updated 3 years ago
• vagarwal87 / Xpresso
  Predicting gene expression levels from genomic sequences
  ☆54Updated 5 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated last month
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆55Updated last month
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated 3 months ago
• bm2-lab / MUSIC
  model-based understanding of single-cell CRISPR screening
  ☆25Updated 10 months ago
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆27Updated last month
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆90Updated last year
• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• frankligy / SNAF
  Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing da…
  ☆49Updated 8 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆181Updated last month
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆17Updated 3 years ago
• Illumina / PromoterAI
  ☆80Updated 4 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆79Updated last week
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆84Updated 4 years ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆33Updated 6 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆33Updated 8 months ago
• gaolabtools / scNanoGPS
  Single cell Nanopore sequencing data for Genotype and Phenotype
  ☆54Updated 5 months ago
• alexfields / ORF-RATER
  Regression-based annotation of protein-coding sequences from ribosome profiling data
  ☆32Updated 5 years ago