Alternatives and similar repositories for bpnet

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

• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆223Updated 3 weeks ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆127Updated 4 months ago
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆160Updated 3 months ago
• kundajelab / tfmodisco
  TF MOtif Discovery from Importance SCOres
  ☆138Updated last year
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆94Updated 3 months ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆230Updated last week
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆231Updated 4 months ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆191Updated 2 weeks ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆104Updated 2 years ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆75Updated 10 months ago
• hms-dbmi / hic-data-analysis-bootcamp
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆198Updated 7 years ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆78Updated 3 weeks ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆223Updated last month
• KrishnaswamyLab / SingleCellWorkshop
  ☆90Updated 4 years ago
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆148Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆97Updated 4 months ago
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆264Updated last month
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆152Updated 2 months ago
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆260Updated this week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆308Updated 4 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆249Updated 6 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 2 years ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆236Updated 3 months ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆215Updated 4 months ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆88Updated 5 years ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆310Updated last month
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆183Updated 4 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆254Updated 6 months ago
• CebolaLab / RNA-seq
  Step-by-step analysis pipeline for RNA-seq data
  ☆119Updated last year
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆205Updated 8 months ago