seqscope / STtools
☆10Updated 2 years ago
Alternatives and similar repositories for STtools:
Users that are interested in STtools are comparing it to the libraries listed below
- This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…☆56Updated this week
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 2 years ago
- Join subcellular Visium HD bins into cells☆85Updated 3 months ago
- ☆33Updated last year
- Significance analysis for clustering single-cell RNA-sequencing data☆113Updated 6 months ago
- ☆30Updated 3 months ago
- BANKSY: spatial clustering☆99Updated last week
- Probabilistic cell segmentation for in situ spatial transcriptomics☆67Updated last week
- Single cell RNA-seq analysis for transcriptomic type characterization☆36Updated last week
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆57Updated last week
- Direct estimation of mean and covariance from single cell RNA seq experiments☆100Updated last month
- characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…☆69Updated 2 years ago
- Latent Embedding Multivariate Regression☆87Updated 4 months ago
- Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration☆91Updated last week
- Methods for decontamination of single cell data☆39Updated last month
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆37Updated 3 months ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆106Updated last month
- R implementation of MULTI-seq sample classification workflow☆61Updated last year
- A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.☆112Updated this week
- AnnData interoperability in R☆72Updated last week
- ☆12Updated 2 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆66Updated last week
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆62Updated 2 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 9 months ago
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆34Updated 2 weeks ago
- R package for pathway analysis in scRNA-seq data☆72Updated 7 months ago
- R package for semi-supervised single-cell data integration☆79Updated last year
- Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".☆98Updated 6 months ago
- ☆31Updated 7 months ago
- scDIOR: Single cell data IO softwaRe☆140Updated 3 years ago