Alternatives and similar repositories for orca

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

• 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
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆63Updated 2 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆43Updated 6 months ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆87Updated 8 months ago
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆30Updated 5 years ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆59Updated 2 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆97Updated 4 months ago
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆78Updated 3 weeks ago
• mostafavilabuw / EnformerAssessment
  ☆23Updated 9 months ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆15Updated last month
• ernstlab / full_stack_ChromHMM_annotations
  Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
  ☆36Updated 10 months ago
• xryanglab / RiboMiner
  a toolset for mining multi-dimensional features of the translatome with ribosome profiling data
  ☆18Updated 4 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆94Updated 3 months ago
• arnavmdas / epiphany
  ☆12Updated 2 years ago
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆42Updated last week
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆38Updated last week
• ay-lab / mustache
  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
  ☆74Updated 4 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆40Updated this week
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆38Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆117Updated 9 months ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated 2 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆44Updated last month
• LieberInstitute / INTERACT
  ☆11Updated 2 years ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆75Updated last month
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆59Updated last year
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated 10 months ago