Alternatives and similar repositories for bilby

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

• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆43Updated 6 months ago
• ML4GLand / SeqData
  Annotated sequence data
  ☆11Updated 11 months ago
• jmschrei / ledidi
  Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
  ☆99Updated 7 months ago
• kundajelab / DART-Eval
  ☆42Updated this week
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆24Updated last year
• kipoi / kipoiseq
  Standard set of data-loaders for training and making predictions for DNA sequence-based models.
  ☆83Updated last year
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated this week
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆22Updated 4 months ago
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆69Updated last year
• move37-labs / nucleobench
  Repository for "NucleoBench: A Large-Scale Benchmark of Neural Nucleic Acid Design Algorithms"
  ☆25Updated 2 months ago
• gagneurlab / dependencies_DNALM
  Code repository for the manuscript: Nucleotide dependency analysis of DNA language models reveals genomic functional elements
  ☆25Updated 10 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated last week
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆91Updated 2 months ago
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆50Updated last year
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆67Updated 9 months ago
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆38Updated 10 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆57Updated 5 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆44Updated last week
• de-Boer-Lab / hashFrag
  A command-line tool to mitigate homology-based data leakage in sequence-to-expression models
  ☆19Updated 3 months ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• mhorlacher / rbpnet
  ☆19Updated last year
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 10 months ago
• czi-ai / transcriptformer
  ☆100Updated 2 months ago
• 1edv / evolution
  This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
  ☆96Updated 2 years ago
• johli / scrambler
  Interpretation by Deep Generative Masking for Biological Sequences
  ☆37Updated 4 years ago
• statbiophys / soNNia
  ☆17Updated 2 months ago
• epigen / KPNN
  Knowledge-primed neural networks
  ☆38Updated 2 years ago
• SchubertLab / epytope
  ☆24Updated last month
• statbiophys / SONIA
  Infer selection pressures on features of amino acid CDR3 sequences.
  ☆24Updated last year
• Karollus / SequenceModelBenchmark
  ☆11Updated 2 years ago