Alternatives and similar repositories for single-cell-pseudotime

Users that are interested in single-cell-pseudotime are comparing it to the libraries listed below

• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆464Updated 6 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆566Updated last month
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆331Updated this week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆378Updated 8 months ago
• Teichlab / cellphonedb
  ☆358Updated 3 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆421Updated 3 weeks ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆439Updated last year
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆538Updated 2 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆431Updated 7 months ago
• theislab / cellrank
  CellRank: dynamics from multi-view single-cell data
  ☆393Updated 2 weeks ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆503Updated 2 weeks ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆466Updated last year
• cole-trapnell-lab / monocle-release
  ☆289Updated 3 years ago
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆733Updated last week
• dynverse / dynbenchmark
  Comparison of methods for trajectory inference on single-cell data 🥇
  ☆213Updated 2 years ago
• KrishnaswamyLab / MAGIC
  MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …
  ☆371Updated 11 months ago
• cole-trapnell-lab / monocle3
  ☆404Updated 2 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆477Updated 4 months ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆428Updated 7 months ago
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆369Updated 3 weeks ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆354Updated last month
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆314Updated 6 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆493Updated 5 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆303Updated 5 years ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆597Updated this week
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆291Updated 2 years ago
• hemberg-lab / scRNA.seq.datasets
  Collection of public scRNA-Seq datasets used by our group
  ☆173Updated 4 years ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆295Updated 2 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆346Updated 9 months ago