Alternatives and similar repositories for perturbation_benchmarking

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

• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆44Updated 8 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆47Updated 3 weeks ago
• emmijokinen / TCRconv
  TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…
  ☆25Updated 2 years ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated this week
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 4 months ago
• mostafavilabuw / EnformerAssessment
  ☆23Updated 11 months ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 4 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆42Updated last week
• 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
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆70Updated 8 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆68Updated last month
• theislab / tcellmatch
  ☆40Updated 4 years ago
• altoslabs / perturbench
  ☆34Updated 2 months ago
• mhorlacher / rbpnet
  ☆18Updated last year
• 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
• epigen / KPNN
  Knowledge-primed neural networks
  ☆38Updated 2 years ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆83Updated last month
• gagneurlab / scooby
  scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
  ☆29Updated last week
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 6 months ago
• brineylab / grp-paper
  Code and data used in The Great Repertoire Project
  ☆30Updated 4 years ago
• BaiDing1234 / AttentionPert
  ☆13Updated last year
• netZoo / netbooks
  Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..
  ☆44Updated 2 weeks ago
• Carldeboer / CisRegModels
  Scripts for building computational models of gene regulation with tensorflow
  ☆10Updated 5 years ago
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆27Updated 2 years ago
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆24Updated 3 months ago
• 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
• theislab / mubind
  Learning motif contributions to cell transitions using sequence features and graphs.
  ☆28Updated 11 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…
  ☆64Updated 2 years ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆51Updated last month