Alternatives and similar repositories for scGEAToolbox

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

• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆52Updated last year
• sqjin / scEpath
  An energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data
  ☆18Updated 4 years ago
• berenslab / umi-normalization
  Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…
  ☆40Updated 3 years ago
• pachterlab / LP_2021
  ☆49Updated last month
• mbernste / SpatialCorr
  SpatialCorr: Identify gene sets with spatially varying correlation
  ☆17Updated last year
• TaylorResearchLab / scedar
  Single-cell exploratory data analysis for RNA-Seq
  ☆40Updated 4 years ago
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆40Updated 6 years ago
• soedinglab / prosstt
  PRObabilistic Simulations of ScRNA-seq Tree-like Topologies
  ☆26Updated last year
• idekerlab / pyNBS
  Python 2.7 implementation of network-based stratification (NBS) algorithm from Hofree et al (Nature Methods 2013)
  ☆37Updated 9 months ago
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆56Updated last year
• AltschulerWu-Lab / scScope
  ☆48Updated 6 years ago
• calico / velodyn
  Dynamical systems methods for RNA velocity analysis
  ☆24Updated 4 years ago
• seasamgo / rescue
  Bootstrap imputation for scRNAseq data
  ☆12Updated 5 years ago
• quadbio / VoxHunt
  VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
  ☆47Updated last year
• willtownes / nsf-paper
  Nonnegative spatial factorization for multivariate count data
  ☆58Updated 2 years ago
• netZoo / netbooks
  Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..
  ☆44Updated 2 weeks ago
• linnarsson-lab / adult-human-brain
  Cytograph version used for adult human-brain analysis
  ☆85Updated last month
• bioFAM / mofapy2
  Multi-omics factor analysis v2
  ☆47Updated 9 months ago
• quon-titative-biology / siVAE
  ☆14Updated last month
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆60Updated last year
• LuyiTian / sc_mixology
  This contains the dataset for comparing scRNA-seq analysis methods
  ☆91Updated 4 years ago
• WangShuxiong / SoptSC
  SoptSC for single cell data analysis: unsupervised inference of clustering, cell lineage, pseudotime and cell-cell communication network …
  ☆22Updated 4 years ago
• hmatsu1226 / SCODE
  SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
  ☆45Updated 5 years ago
• txWang / BERMUDA
  BERMUDA (Batch Effect ReMoval Using Deep Autoencoders) is a novel transfer-learning-based method for batch correction in scRNA-seq data.
  ☆31Updated 5 years ago
• zhoujt1994 / scHiCluster
  ☆67Updated 2 months ago
• GreenleafLab / motifmatchr
  Fast motif matching in R
  ☆46Updated last year
• LungCellAtlas / mapping_data_to_the_HLCA
  Repository to perform mapping of new datasets to the Human Lung Cell Atlas.
  ☆19Updated 2 years ago
• dgrun / RaceID3_StemID2_package
  Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and S…
  ☆43Updated 8 months ago
• ma-compbio / SpiceMix
  spatial transcriptome, single cell
  ☆69Updated 2 years ago
• pqiu / cooccurrence_clustering
  ☆13Updated 5 years ago