Alternatives and similar repositories for DIRECT-NET:

Users that are interested in DIRECT-NET are comparing it to the libraries listed below

• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆23Updated 3 weeks ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆40Updated 3 months ago
• ratschlab / scim
  Code for Universal Single-Cell Matching with Unpaired Feature Sets
  ☆21Updated 3 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 11 months ago
• wycwycpku / RSCORE
  ☆25Updated 3 years ago
• jingshuw / SAVERX
  R package for transfer learning of single-cell RNA-seq denoising
  ☆30Updated 2 years ago
• josephreplogle / guide_calling
  Tools for sgRNA calling in direct capture Perturb-seq data
  ☆32Updated last year
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆34Updated 4 years ago
• decomverse / ACTIONet
  ACTIONet single-cell analysis framework
  ☆38Updated 6 months ago
• CostaLab / scMEGA
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
  ☆38Updated 6 months ago
• CostaLab / scopen
  scOpen: single-cell open chromatin analysis via NMF modelling
  ☆26Updated 2 years ago
• kaizhang / single-cell-benchmark
  ☆10Updated last year
• GreenleafLab / brainchromatin
  Code used to analyze single cell RNA and ATAC sequencing in developing human brain
  ☆33Updated 3 years ago
• caleblareau / asap_reproducibility
  Reproducing all analyses and figures for the ASAP-seq paper
  ☆29Updated 3 years ago
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆24Updated 2 years ago
• PMBio / scNMT-seq
  single-cell Nucleosome Methylation Transcription
  ☆13Updated 7 years ago
• gambalab / gficf
  An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization
  ☆18Updated last year
• AllonKleinLab / cospar
  ☆26Updated last year
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆41Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆48Updated this week
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆34Updated 3 years ago
• zhouzilu / cTPnet
  cTPnet Package
  ☆25Updated 2 years ago
• raphael-group / netNMF-sc
  netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data
  ☆22Updated 3 years ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated last year
• PeterZZQ / CellPath
  ☆21Updated 2 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆27Updated 4 months ago
• csjansen / SOMatic
  SOMatic is a tool for building Self-Organizing Maps and linking multiple maps.
  ☆14Updated 7 months ago
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• pachterlab / GFCP_2022
  RNA velocity validation
  ☆22Updated 3 years ago