Alternatives and similar repositories for semla

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

• pachterlab / voyager
  From geospatial to spatial -omics
  ☆98Updated last month
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆81Updated 3 years ago
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆81Updated last year
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆90Updated 4 months ago
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆82Updated this week
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆90Updated 5 months ago
• guokai8 / scGSVA
  scGSVA: Perform GSVA for single cell RNA seq
  ☆66Updated last year
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆76Updated last year
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆90Updated 3 months ago
• saezlab / mistyR
  Multiview Intercellular SpaTial modeling framework
  ☆71Updated 5 months ago
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆52Updated last year
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆57Updated 2 weeks ago
• alserglab / mascarade
  Generate masks for scRNA-seq clusters on t-SNE or UMAP plots
  ☆36Updated this week
• JEFworks-Lab / CRAWDAD
  Cell-type Relationship Analysis Workflow Done Across Distances
  ☆37Updated 5 months ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆74Updated this week
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆44Updated this week
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆131Updated 3 months ago
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆92Updated 10 months ago
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆87Updated last week
• const-ae / lemur
  Latent Embedding Multivariate Regression
  ☆97Updated 11 months ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆76Updated 3 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆122Updated this week
• theislab / destiny
  R package for single cell and other data analysis using diffusion maps
  ☆89Updated this week
• zktuong / ktplotspy
  Python library for plotting Cellphonedb results. Ported from ktplots R package.
  ☆56Updated this week
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆83Updated 2 years ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆64Updated 3 years ago
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆30Updated last year
• Nanostring-Biostats / GeomxTools
  Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.…
  ☆45Updated last month
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆33Updated last year
• Oshlack / speckle
  R package for specialised analysis of single cell data
  ☆39Updated 3 years ago