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.
  ☆70Updated 7 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆97Updated 2 years ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆140Updated 2 weeks ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆122Updated 2 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆26Updated 3 weeks ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆55Updated last month
• kundajelab / bpnet
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
  ☆150Updated 6 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…
  ☆57Updated last year
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆47Updated this week
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆35Updated 3 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆67Updated last week
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆38Updated last month
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆99Updated last month
• tkzeng / Pangolin
  Pangolin is a deep-learning method for predicting splice site strengths.
  ☆67Updated 8 months ago
• epigen / CellWhisperer
  CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets
  ☆50Updated 4 months ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆15Updated last year
• YosefLab / popV
  ☆69Updated last week
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆76Updated 4 months ago
• kundajelab / DART-Eval
  ☆27Updated last month
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆85Updated 4 months ago
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆29Updated 5 years ago
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆77Updated 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
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆207Updated 2 months ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆126Updated 3 weeks ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆57Updated last week
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated 9 months ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆16Updated last month
• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆115Updated 2 years ago
• rnakato / ShortCake
  A docker image for single-cell analysis
  ☆81Updated 2 weeks ago