Alternatives and similar repositories for spectra

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

• dpeerlab / SEACells
  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
  ☆168Updated 6 months ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆111Updated last year
• icbi-lab / infercnvpy
  Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
  ☆173Updated last week
• digitalcytometry / cytospace
  CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data
  ☆133Updated 8 months ago
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆113Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆113Updated last year
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆142Updated 2 years ago
• changwn / scFEA
  single cell Flux Estimation Analysis (scFEA) Try the below web server!
  ☆133Updated last year
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆74Updated 8 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆128Updated last year
• JEFworks-Lab / STdeconvolve
  Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
  ☆146Updated 2 months ago
• saeyslab / multinichenetr
  MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…
  ☆166Updated 2 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆147Updated 10 months ago
• YosefLab / Compass
  In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
  ☆117Updated this week
• YosefLab / popV
  ☆83Updated this week
• theislab / scCODA
  A Bayesian model for compositional single-cell data analysis
  ☆177Updated 2 years ago
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆176Updated last year
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆74Updated this week
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆229Updated this week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆122Updated 2 weeks ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆236Updated 9 months ago
• YMa-lab / CARD
  ☆126Updated last year
• zcang / COMMOT
  ☆124Updated last year
• SONGDONGYUAN1994 / scDesign3
  scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
  ☆106Updated 3 weeks ago
• saezlab / liana-py
  LIANA+: an all-in-one framework for cell-cell communication
  ☆241Updated last week
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆188Updated this week
• navinlabcode / CellTrek
  ☆125Updated 3 years ago
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆139Updated last week
• rajewsky-lab / novosparc
  ☆131Updated last year
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆111Updated 7 months ago