Alternatives and similar repositories for paga:

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

• Teichlab / bbknn
  Batch balanced KNN
  ☆160Updated last year
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆206Updated last year
• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆158Updated last month
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆168Updated last week
• kharchenkolab / conos
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆211Updated last year
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆173Updated 3 weeks ago
• quadbio / Pando
  Multiome GRN inference.
  ☆121Updated last year
• theislab / kBET
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆162Updated last year
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆163Updated 2 years ago
• CahanLab / singleCellNet
  SingleCellNet: classify single cells across species and platforms
  ☆137Updated last year
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆144Updated 5 months ago
• swolock / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆149Updated 4 years ago
• rajewsky-lab / novosparc
  ☆128Updated last year
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated 2 months ago
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆127Updated 2 months ago
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆226Updated 3 weeks ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆201Updated 9 months ago
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆121Updated 2 years ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆291Updated last year
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆131Updated 6 months ago
• slowkow / harmonypy
  🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.
  ☆217Updated 10 months ago
• YosefLab / VISION
  Signature Analysis and Visualization for Single-Cell RNA-seq
  ☆165Updated 11 months ago
• dynverse / dynmethods
  A collection of 50+ trajectory inference methods within a common interface 📥📤
  ☆127Updated last year
• aertslab / cisTopic
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
  ☆139Updated last year
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆279Updated last year
• csoneson / conquer_comparison
  Code for evaluation of differential expression methods in single-cell RNA-seq data
  ☆112Updated 4 years ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆110Updated 6 months ago
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆153Updated this week
• dpeerlab / spectra
  Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
  ☆168Updated 9 months ago
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆193Updated last week