Alternatives and similar repositories for scTDA:

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

• KrishnaswamyLab / scprep
  A collection of scripts and tools for loading, processing, and handling single cell data.
  ☆72Updated last year
• RabadanLab / scTDA
  An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data
  ☆7Updated 7 years ago
• simslab / scHPF
  Single-cell Hierarchical Poisson Factorization
  ☆69Updated 2 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 2 years ago
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆40Updated 6 years ago
• KrishnaswamyLab / MELD
  Quantifying experimental perturbations at single cell resolution
  ☆105Updated 6 months ago
• bioFAM / slalom
  ☆28Updated 2 years ago
• MarioniLab / Deconvolution2016
  Code and manuscript files for Aaron and Karsten's deconvolution paper.
  ☆16Updated 6 years ago
• aristoteleo / Scribe-py
  Regulatory networks with Direct Information in python
  ☆40Updated 2 years ago
• willtownes / glmpca-py
  generalized principal component analysis (GLM-PCA) implemented in python
  ☆60Updated 4 years ago
• AllenInstitute / MTG_celltypes
  Human cortical cell types
  ☆24Updated 5 years ago
• Murali-group / BoolODE
  Git Repo for simulating Boolean Models
  ☆33Updated 10 months ago
• dawe / schist
  An interface for Nested Stochastic Block Model for single cell analysis
  ☆32Updated last month
• gdurif / pCMF
  pCMF R package
  ☆14Updated 6 years ago
• AllonKleinLab / PBA
  Population balance analysis
  ☆44Updated 5 years ago
• czi-hca-comp-tools / easy-data
  easy access to benchmark datasets
  ☆50Updated 6 years ago
• stanleyn / Comp790-166-Comp-Bio
  Computational Biology- Spring 2021
  ☆46Updated 3 years ago
• yanailab / knn-smoothing
  K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data
  ☆55Updated 2 years ago
• hmatsu1226 / SCODE
  SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
  ☆43Updated 5 years ago
• klarman-cell-observatory / scPhere
  ☆99Updated 2 years ago
• cantinilab / OT-scOmics
  This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in…
  ☆38Updated 2 years ago
• jessica1338 / CSHMM-for-time-series-scRNA-Seq
  This is the code release for paper Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data
  ☆22Updated 7 years ago
• Tchanders / network_inference_tutorials
  ☆31Updated 5 years ago
• cole-trapnell-lab / Scribe
  Regulatory networks with Direct Information
  ☆16Updated 5 years ago
• kylessmith / dynamicTreeCut
  Python translation of the hybrid dynamicTreeCut method as created by Peter Langfelder and Bin Zhang.
  ☆40Updated 3 years ago
• netZoo / netbooks
  Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..
  ☆40Updated last month
• AltschulerWu-Lab / scScope
  ☆49Updated 5 years ago
• YosefLab / SymSim
  ☆25Updated 6 months ago
• Teichlab / MultiMAP
  MultiMAP for integration of single cell multi-omics
  ☆55Updated last year
• swoodhouse / SCNS-Toolkit
  Single cell network synthesis toolkit
  ☆23Updated 4 years ago