Alternatives and similar repositories for gopher:

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

• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆38Updated 4 months ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆24Updated this week
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆30Updated last month
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆46Updated this week
• vagarwal87 / saluki_paper
  Saluki, a method to predict mRNA half-lives from sequence
  ☆22Updated 2 years ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆56Updated last week
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆37Updated 3 weeks ago
• MiraldiLab / maxATAC
  Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
  ☆28Updated this week
• kundajelab / ProCapNet
  Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
  ☆13Updated this week
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆14Updated this week
• viannegao / ChromaFold
  ☆25Updated 6 months ago
• mostafavilabuw / EnformerAssessment
  ☆19Updated 7 months ago
• liu-bioinfo-lab / EPCOT
  ☆21Updated last year
• jzhoulab / puffin_manuscript
  ☆17Updated 5 months ago
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆16Updated 3 years ago
• theislab / tcellmatch
  ☆38Updated 4 years ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆31Updated last week
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆18Updated last week
• mhorlacher / rbpnet
  ☆18Updated last year
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆26Updated 2 years ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆32Updated last year
• 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
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆47Updated last week
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆71Updated last month
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆23Updated 3 weeks ago
• dpeerlab / scKINETICS
  Code for scKINETICS (ISMB 2023)
  ☆21Updated last year
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆27Updated 2 months ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆27Updated last year
• 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…
  ☆35Updated last week
• neurogenomics / EnformerCelltyping
  Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…
  ☆13Updated 4 months ago