Alternatives and similar repositories for spatialTCR

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

• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆78Updated 2 months ago
• 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
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆76Updated 9 months ago
• Banovich-Lab / Spatial_PF
  ☆32Updated last month
• jfnavarro / st_pipeline
  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …
  ☆88Updated 9 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆44Updated 3 months ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated 7 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 5 months ago
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆123Updated 7 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆81Updated 8 months ago
• YosefLab / popV
  ☆84Updated last week
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆62Updated 3 months ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆82Updated 10 months ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆28Updated last year
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆57Updated 2 years ago
• snehamitra / SCARlink
  ☆59Updated 5 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆97Updated 11 months ago
• data2intelligence / CytoSig
  ☆59Updated last year
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆62Updated last year
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆115Updated last month
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆38Updated 4 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆105Updated last year
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆65Updated last year
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆123Updated 2 weeks ago
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆71Updated last year
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆116Updated last year
• jaleesr / SenePy
  SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following pu…
  ☆45Updated 10 months ago
• di-0579 / Spatial_epigenome-transcriptome_co-sequencing
  ☆33Updated 2 years ago