scType goes spatial: ScType enables fast and accurate cell type identification from spatial transcriptomics data
☆11Jul 11, 2024Updated last year
Alternatives and similar repositories for sp-type
Users that are interested in sp-type are comparing it to the libraries listed below
Sorting:
- scType rewritten in python☆25Nov 7, 2024Updated last year
- Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data☆30Updated this week
- v1.0☆14Aug 1, 2025Updated 7 months ago
- Cell clustering and communication network inference for single-cell transcriptomics☆14Sep 18, 2024Updated last year
- ☆12Nov 6, 2023Updated 2 years ago
- Functions to analyze copy number aberrations in single-cell data☆13Feb 3, 2025Updated last year
- Identification of clone-specific and cancer-selective multi-targeting therapeutic options based on single-cell transcriptomic profiles of…☆19Feb 20, 2025Updated last year
- single-cell Contamination Detection and Correction☆17Jan 15, 2025Updated last year
- Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data☆17Apr 15, 2025Updated 10 months ago
- Codes used in LISTA project.☆15Apr 17, 2024Updated last year
- BICSEQ2 pipeline for processing CPTAC3 somatic WGS CNA☆16Apr 13, 2021Updated 4 years ago
- Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalsc…☆27Sep 30, 2025Updated 5 months ago
- ☆25Feb 20, 2025Updated last year
- Spatial transcriptome analysis in python☆25Jan 26, 2025Updated last year
- Automatic selection of number of principal components☆17Jun 27, 2022Updated 3 years ago
- STRIDE (Spatial TRanscRIptomics DEconvolution by topic modelling) is a cell-type deconvolution tool for spatial transcriptomics by using …☆17Aug 12, 2022Updated 3 years ago
- Join subcellular Visium HD bins into cells☆137Nov 4, 2025Updated 4 months ago
- Analysis pipeline for CUT&TAG data☆23Sep 2, 2020Updated 5 years ago
- ☆285Nov 10, 2024Updated last year
- ☆19Sep 18, 2019Updated 6 years ago
- Interoperability between SpatialData and the Xenium Explorer☆25Jul 31, 2024Updated last year
- MERFISH decoding software☆26Aug 16, 2025Updated 6 months ago
- material related to the genetech courses☆10Sep 11, 2023Updated 2 years ago
- Repository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcript…☆31Jul 13, 2024Updated last year
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆151Nov 23, 2025Updated 3 months ago
- ☆21May 6, 2025Updated 9 months ago
- Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries☆12Jan 4, 2026Updated last month
- Detection and classification selective sweep use domain adaptive model☆10Apr 29, 2024Updated last year
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆33Apr 4, 2025Updated 11 months ago
- CORNAS is a fast method for reliable DEG calls in unreplicated conditions.☆13Jul 14, 2019Updated 6 years ago
- mesa package for Methylation Enrichment Sequencing Analysis☆15Nov 20, 2025Updated 3 months ago
- 10X single cell Nanopore reads simulation workflow. Complete documentation avialable at: https://GenomiqueENS.github.io/AsaruSim/☆13Jul 27, 2025Updated 7 months ago
- ☆11Feb 2, 2026Updated last month
- ☆10May 31, 2022Updated 3 years ago
- Analysis of smFISH data☆12Aug 27, 2018Updated 7 years ago
- Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA☆84Apr 21, 2025Updated 10 months ago
- ☆38Oct 25, 2018Updated 7 years ago
- A robust DE test method that accounts for the uncertainty in pseudotime inference☆39Mar 2, 2025Updated last year
- Cell-type Relationship Analysis Workflow Done Across Distances☆41Nov 18, 2025Updated 3 months ago