Alternatives and similar repositories for DeepSTARR

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

• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆84Updated last week
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 6 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 8 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆79Updated last year
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆49Updated last month
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated 2 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆96Updated 7 months ago
• vagarwal87 / saluki_paper
  Saluki, a method to predict mRNA half-lives from sequence
  ☆25Updated 2 years ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 10 months ago
• vagarwal87 / Xpresso
  Predicting gene expression levels from genomic sequences
  ☆54Updated 5 years ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆92Updated 7 months ago
• Illumina / PromoterAI
  ☆77Updated 3 months ago
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆70Updated 10 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆55Updated last month
• StatBiomed / CamoTSS
  Detection and couting alternative TSS in single cells
  ☆15Updated last year
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• ernstlab / full_stack_ChromHMM_annotations
  Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
  ☆37Updated last year
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆89Updated last year
• vanallenlab / comut
  CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
  ☆95Updated last year
• alexfields / ORF-RATER
  Regression-based annotation of protein-coding sequences from ribosome profiling data
  ☆32Updated 5 years ago
• tkzeng / Pangolin
  Pangolin is a deep-learning method for predicting splice site strengths.
  ☆79Updated last year
• GuanLab / Anchor
  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
• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• bm2-lab / MUSIC
  model-based understanding of single-cell CRISPR screening
  ☆25Updated 9 months ago
• mdozmorov / ChIP-seq_notes
  Notes on ChIP-seq and other-seq-related tools
  ☆26Updated 2 months ago
• andrewrech / antigen.garnish
  ☆49Updated 3 years ago
• bernardo-de-almeida / motif-clustering
  Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy
  ☆27Updated 2 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated last week
• aertslab / CREsted
  CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…
  ☆47Updated last month