Alternatives and similar repositories for puffin

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

• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆78Updated last year
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆31Updated 6 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆108Updated 2 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆44Updated 9 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆84Updated 2 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆70Updated last month
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 4 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆177Updated last month
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 9 months ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆65Updated 2 years ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆47Updated last month
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆91Updated 5 months ago
• Illumina / PromoterAI
  ☆70Updated 2 months ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆236Updated last month
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆86Updated 2 weeks ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆86Updated 10 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 4 months ago
• kundajelab / DART-Eval
  ☆38Updated last month
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆187Updated 2 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 7 months ago
• kundajelab / bpnet
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
  ☆161Updated 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
• chengl7-lab / kmap
  A tool for visualising kmers in 2D space.
  ☆10Updated 6 months ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated last month
• jzhoulab / puffin_manuscript
  ☆17Updated 10 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆22Updated 3 months ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆16Updated 3 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 7 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆51Updated last month
• seqcode / cross-species-domain-adaptation
  Codebase for the domain adaptation (cross-species TF binding prediction) project.
  ☆12Updated 2 years ago