Alternatives and similar repositories for puffin:

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

• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆56Updated last week
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆100Updated 2 years ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆74Updated 9 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆27Updated 2 months ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆137Updated 2 weeks ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆151Updated 2 months ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆67Updated 2 weeks ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆41Updated 4 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆71Updated last month
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆61Updated last year
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆46Updated last week
• tkzeng / Pangolin
  Pangolin is a deep-learning method for predicting splice site strengths.
  ☆72Updated 9 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆37Updated 3 weeks ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆15Updated last month
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆47Updated 2 weeks ago
• mostafavilabuw / EnformerAssessment
  ☆19Updated 7 months ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆17Updated 2 months ago
• kundajelab / DART-Eval
  ☆33Updated this week
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆213Updated 3 weeks ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆85Updated 6 months ago
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆80Updated 2 years ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆97Updated 2 months ago
• YeoLab / eCLIP
  ☆37Updated 2 years ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆127Updated 2 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆82Updated last month
• uio-bmi / immuneML
  immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
  ☆67Updated this week
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated last week
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆91Updated 4 years ago
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated 11 months ago