Alternatives and similar repositories for WEDGE:

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

• raphael-group / netNMF-sc
  netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data
  ☆22Updated 4 years ago
• IlyaLab / gssnng
  Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.
  ☆12Updated 6 months ago
• WangShuxiong / SoptSC
  SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network …
  ☆21Updated 4 years ago
• mukamel-lab / SingleCellFusion
  SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data
  ☆12Updated 3 years ago
• PeterZZQ / CellPath
  ☆21Updated 2 years ago
• zhanglhbioinfor / DIRECT-NET
  ☆10Updated last year
• AllonKleinLab / paper-data
  ☆20Updated 3 weeks ago
• quadbio / organoid_regulomes
  Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids
  ☆28Updated last year
• yycunc / SAFEclustering
  SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data
  ☆17Updated 4 years ago
• mohuangx / SAVER-paper
  Scripts for data and figure generation in SAVER paper
  ☆17Updated 4 years ago
• dyxmvp / Spatial_ATAC-seq
  ☆22Updated 2 years ago
• almaan / ST-mLiver
  Code associated with the manuscript Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in t…
  ☆17Updated 2 years ago
• RegnerM2015 / scBreast_scRNA_scATAC_2024
  Repository to store code used for the analyses presented in "Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic …
  ☆13Updated last month
• tarot0410 / BREMSC
  Novel joint clustering method with scRNA-seq and CITE-seq data
  ☆9Updated 3 years ago
• SunXQlab / ESICCC
  ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods
  ☆12Updated last year
• gitter-lab / SINGE
  Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
  ☆11Updated 9 months ago
• AmandaKedaigle / OrganoidAtlas
  Code to go along with https://doi.org/10.1016/j.cell.2022.09.010
  ☆20Updated 3 years ago
• bioinfoDZ / RISC
  A R package for integrated scRNA-seq data analysis using the RPCI algorithm
  ☆44Updated last year
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆34Updated 4 years ago
• KChen-lab / bindSC
  Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…
  ☆34Updated last year
• quadbio / simspec
  Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
  ☆31Updated last year
• PeterZZQ / scMoMaT
  ☆21Updated 10 months ago
• wycwycpku / RSCORE
  ☆25Updated 3 years ago
• wanglabtongji / STRIDE
  STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using …
  ☆27Updated last year
• saezlab / FootprintMethods_on_scRNAseq
  Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
  ☆26Updated 5 years ago
• SunXQlab / scMLnet
  Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
  ☆26Updated 3 years ago
• zhengtaoxiao / Single-Cell-Metabolic-Landscape
  Pipeline for characterizing metebolic heterogeneity from single-cell RNA-seq data
  ☆22Updated 3 years ago
• netbiolab / scHumanNet
  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3
  ☆41Updated last year
• sqjin / scAI
  An unsupervised approach for the integrative analysis of single-cell multi-omics data
  ☆29Updated 4 years ago
• BIOINSu / SNN-Cliq
  An algorithm used to classify the cell types from single cell rna sequence data.
  ☆10Updated 4 years ago