Alternatives and similar repositories for ZIFA

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

• BatzoglouLabSU / SIMLR
  Implementations in both Matlab and R of the SIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/n…
  ☆113Updated 4 months ago
• simslab / scHPF
  Single-cell Hierarchical Poisson Factorization
  ☆73Updated 3 years ago
• mohuangx / SAVER
  Single-cell RNA-seq Gene Expression Recovery
  ☆111Updated 9 months ago
• 10XGenomics / single-cell-3prime-paper
  ☆85Updated 5 years ago
• AltschulerWu-Lab / scScope
  ☆48Updated 6 years ago
• LuyiTian / sc_mixology
  This contains the dataset for comparing scRNA-seq analysis methods
  ☆91Updated 5 years ago
• Vivianstats / scImpute
  Accurate and robust imputation of scRNA-seq data
  ☆96Updated 6 years ago
• dynverse / dynverse
  A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
  ☆76Updated 4 years ago
• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆74Updated last month
• hemberg-lab / SC3
  A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
  ☆128Updated 4 years ago
• czi-hca-comp-tools / easy-data
  easy access to benchmark datasets
  ☆50Updated 7 years ago
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆141Updated last year
• campbio / celda
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆149Updated 6 months ago
• linnarsson-lab / BackSPIN
  Biclustering algorithm
  ☆56Updated 7 years ago
• jacoblevine / PhenoGraph
  Subpopulation detection in high-dimensional single-cell data
  ☆137Updated 4 years ago
• bioFAM / slalom
  ☆29Updated 2 years ago
• romain-lopez / scVI-reproducibility
  Reproducing the experiments of the paper "Deep generative modeling for single-cell transcriptomics"
  ☆57Updated 6 years ago
• wang-research / VASC
  Variational autoencoder for single cell RNA-seq datasets
  ☆44Updated 8 years ago
• PMBio / scLVM
  scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…
  ☆107Updated 2 years ago
• KrishnaswamyLab / phateR
  PHATE dimensionality reduction method implemented in R
  ☆78Updated 4 years ago
• chriscainx / mnnpy
  An implementation of MNN (Mutual Nearest Neighbors) correct in python.
  ☆74Updated 2 years ago
• scverse / scanpy_usage
  Scanpy use cases.
  ☆86Updated 4 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆94Updated 6 years ago
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆89Updated 10 months ago
• yanailab / knn-smoothing
  K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data
  ☆56Updated 2 years ago
• sandhya212 / BISCUIT_SingleCell_IMM_ICML_2016
  R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.
  ☆66Updated 7 years ago
• aertslab / arboreto
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
  ☆60Updated last year
• klarman-cell-observatory / scPhere
  ☆101Updated 2 years ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆169Updated last year
• slowkow / tftargets
  Human transcription factor target genes from 6 databases in convenient R format.
  ☆86Updated 6 years ago