Alternatives and similar repositories for spacemake

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

• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 4 months ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆56Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 6 months ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆68Updated last week
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 3 years ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆109Updated 2 weeks ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆91Updated 6 months ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆62Updated 3 months ago
• UPSUTER / GEMLI
  ☆32Updated 10 months ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated 3 months ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆66Updated 3 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆86Updated 7 months ago
• ajaynadig / TRADEtools
  ☆33Updated 8 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆44Updated 2 years ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆64Updated 2 years ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆29Updated 8 months ago
• jbergenstrahle / STUtility
  ☆53Updated 2 years ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated 7 months ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆123Updated last week
• HYsxe / PRINT
  ☆37Updated last year
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆81Updated 8 months ago
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆50Updated last year
• anders-biostat / MethSCAn
  Python package with CLI for the analysis of single cell methylation data.
  ☆18Updated last year
• YosefLab / Cassiopeia
  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
  ☆97Updated last week
• cellatlas / human
  ☆44Updated last year
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆44Updated 3 years ago
• almaan / eggplant
  ☆22Updated 3 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆76Updated 9 months ago