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.
  ☆76Updated 3 months ago
• simslab / scHPF
  Single-cell Hierarchical Poisson Factorization
  ☆74Updated 3 years ago
• yanailab / knn-smoothing
  K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data
  ☆60Updated 3 years ago
• epierson9 / ZIFA
  Zero-inflated dimensionality reduction algorithm for single-cell data
  ☆111Updated 5 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
• KrishnaswamyLab / MELD
  Quantifying experimental perturbations at single cell resolution
  ☆112Updated last year
• bioFAM / slalom
  ☆29Updated 2 years ago
• czi-hca-comp-tools / easy-data
  easy access to benchmark datasets
  ☆50Updated 7 years ago
• theislab / pseudodynamics
  Dynamic models for single-cell RNA-seq time series.
  ☆40Updated 7 years ago
• RabadanLab / randomly
  A Library for Denoising Single-Cell Data with Random Matrix Theory
  ☆37Updated 2 years ago
• BIRSBiointegration / Hackathon
  Multi-omics studies are available here
  ☆52Updated 3 years ago
• aristoteleo / Scribe-py
  Regulatory networks with Direct Information in python
  ☆40Updated 2 years ago
• dawe / schist
  An interface for Nested Stochastic Block Model for single cell analysis
  ☆36Updated 3 months ago
• swoodhouse / SCNS-Toolkit
  Single cell network synthesis toolkit
  ☆23Updated 4 years ago
• willtownes / glmpca-py
  generalized principal component analysis (GLM-PCA) implemented in python
  ☆61Updated 4 years ago
• 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 3 months ago
• pachterlab / picasso
  Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.
  ☆71Updated 3 months ago
• broadinstitute / wot
  A software package for analyzing snapshots of developmental processes
  ☆151Updated 3 years ago
• dynverse / dyngen
  Simulating single-cell data using gene regulatory networks 📠
  ☆78Updated last year
• AltschulerWu-Lab / scScope
  ☆48Updated 6 years ago
• ushaham / BatchEffectRemoval
  ☆56Updated 5 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…
  ☆42Updated 2 years ago
• SchulzLab / TEPIC
  Annotation of genomic regions using transcription factor binding sites and epigenetic data
  ☆41Updated 3 years ago
• KrishnaswamyLab / phateR
  PHATE dimensionality reduction method implemented in R
  ☆81Updated 4 years ago
• nolanlab / vortex
  VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:
  ☆34Updated 2 years ago
• AllonKleinLab / PBA
  Population balance analysis
  ☆44Updated 6 years ago
• klarman-cell-observatory / scPhere
  ☆101Updated 2 years ago
• BIMSBbioinfo / maui
  Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
  ☆50Updated 2 years ago
• stanleyn / Comp790-166-Comp-Bio
  Computational Biology- Spring 2021
  ☆48Updated 4 years ago
• KrishnaswamyLab / SAUCIE
  ☆102Updated last year