Alternatives and similar repositories for GENIE3

Users that are interested in GENIE3 are comparing it to the libraries listed below

• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆89Updated 11 months ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆95Updated 6 years ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆53Updated last year
• gao-lab / Cell_BLAST
  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
  ☆93Updated last year
• SUwonglab / PECA
  PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
  ☆45Updated last week
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆89Updated 10 months ago
• hmatsu1226 / SCODE
  SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
  ☆45Updated 5 years ago
• jsxlei / SCALE
  Single-cell ATAC-seq analysis via Latent feature Extraction
  ☆102Updated 2 years ago
• Vivianstats / scImpute
  Accurate and robust imputation of scRNA-seq data
  ☆97Updated 6 years ago
• smaslova / AI-TAC
  ☆27Updated 2 years ago
• jsxlei / SCALEX
  Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
  ☆79Updated last week
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆78Updated last year
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆59Updated last year
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆150Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 10 months ago
• decomverse / ACTIONet
  ACTIONet single-cell analysis framework
  ☆42Updated last year
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆119Updated 3 years ago
• zhoujt1994 / scHiCluster
  ☆68Updated 3 months ago
• rajewsky-lab / novosparc
  ☆131Updated last year
• velocyto-team / velocyto-notebooks
  ☆56Updated 7 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated last week
• califano-lab / ARACNe-AP
  Network Reverse Engineering through AP inference of Mutual Information
  ☆86Updated 2 years ago
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆102Updated 6 months ago
• saeyslab / moduledetection-evaluation
  ☆33Updated 3 years ago
• Durenlab / LINGER
  ☆114Updated 3 months ago
• KlugerLab / ALRA
  Imputation method for scRNA-seq based on low-rank approximation
  ☆77Updated last year
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆67Updated 2 years ago
• broadinstitute / Celligner_ms
  Code related to the Celligner manuscript
  ☆46Updated 4 years ago
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆18Updated 3 years ago