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.
  ☆75Updated 9 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆102Updated 2 years ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆157Updated 2 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆41Updated 5 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆27Updated 3 months ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆219Updated last week
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆56Updated 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…
  ☆63Updated 2 years ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆72Updated 2 months ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆143Updated last month
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆69Updated last week
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆97Updated 3 months ago
• mostafavilabuw / EnformerAssessment
  ☆19Updated 8 months ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆86Updated 7 months ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆15Updated last week
• tkzeng / Pangolin
  Pangolin is a deep-learning method for predicting splice site strengths.
  ☆73Updated 10 months 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
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆47Updated last month
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆48Updated last week
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆80Updated 2 years ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆127Updated 3 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆39Updated last month
• kundajelab / bpnet
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
  ☆151Updated 9 months ago
• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆118Updated 2 years ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated this week
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆25Updated this week
• kundajelab / DART-Eval
  ☆34Updated this week
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆77Updated 6 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆35Updated last week
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 6 months ago