Alternatives and similar repositories for CpGPT

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

• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆68Updated last month
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 4 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆106Updated 2 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆44Updated 8 months ago
• BergmannLab / MONET
  MONET : MOdularising NEtwork Toolbox - https://doi.org/10.1093/bioinformatics/btaa236
  ☆45Updated 3 years ago
• johli / aparent
  APA Regression Net - Predict and Engineer Alternative Polyadenylation
  ☆39Updated 3 years ago
• MaayanLab / blitzgsea
  Fast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for …
  ☆51Updated 2 months ago
• ShenLab-Genomics / SpliceTransformer
  SpliceTransformer(SpTransformer) is a deep learning tool to predict tissue specific splicing site from pre-mRNA sequence
  ☆27Updated 8 months ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated this week
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 4 months ago
• vagarwal87 / Xpresso
  Predicting gene expression levels from genomic sequences
  ☆53Updated 5 years ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 5 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆31Updated 6 months ago
• 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…
  ☆43Updated this week
• epigen / KPNN
  Knowledge-primed neural networks
  ☆38Updated 2 years ago
• MaayanLab / archs4py
  Python package to load and query ARCHS4 data
  ☆23Updated 2 weeks ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆19Updated 3 months ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆17Updated 2 months ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆84Updated 2 weeks ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 6 months ago
• broadinstitute / depmap_omics
  What you need to process the Quarterly DepMap-Omics releases from Terra
  ☆119Updated this week
• gregbellan / Stabl
  ☆63Updated 8 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆42Updated last week
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆34Updated 4 months ago
• Illumina / PromoterAI
  ☆67Updated last month
• epigen / CellWhisperer
  CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets
  ☆59Updated 9 months ago
• CompEpigen / methylbert
  A Transformer-based model for read-level DNA methylation pattern identification and tumour deconvolution
  ☆35Updated 4 months ago
• uio-bmi / immuneML
  immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
  ☆68Updated this week
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆47Updated 3 weeks ago
• s175573 / DeepCAT
  Deep Learning Method to Identify Cancer Associated TCRs
  ☆47Updated 3 years ago