Alternatives and similar repositories for bpnet

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

• kundajelab / tfmodisco
  TF MOtif Discovery from Importance SCOres
  ☆156Updated last week
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆132Updated 9 months ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆258Updated 3 weeks ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆98Updated 8 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆189Updated 2 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆81Updated last year
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated last month
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆233Updated last month
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆93Updated 8 months ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆202Updated 2 months ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆239Updated 4 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆33Updated 9 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆82Updated last month
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆296Updated 2 weeks ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆235Updated 10 months ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆200Updated 4 months ago
• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆121Updated 2 months ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆248Updated this week
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆52Updated 3 weeks ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆103Updated 2 years ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• urmi-21 / pyrpipe
  Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
  ☆84Updated 4 years ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆71Updated 2 years ago
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• gpp-rnd / rs3
  Package to Score Sequences using Rule Set 3
  ☆12Updated last week
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• uio-bmi / immuneML
  immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
  ☆72Updated last week
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 2 months ago