Pipeline for SpatialTranscriptomics and 10X Visium data
☆22Jul 22, 2025Updated last year
Alternatives and similar repositories for sttkit
Users that are interested in sttkit are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data☆32Dec 22, 2022Updated 3 years ago
- ☆17Sep 16, 2024Updated 2 years ago
- Code required to reproduce analysis of the single cell Cut and Tag data in the resource paper (Bartosovic et. al., 2020)☆16Apr 2, 2026Updated 6 months ago
- Spatial transcriptomics of heart tissue☆114Oct 7, 2023Updated 3 years ago
- CCCvelo: Decoding dynamic cell-cell communication-driven cell state transitions in spatial transcriptomics☆13Sep 14, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- a simple R data package for curated cancer pathway-specific gene lists☆14Mar 31, 2020Updated 6 years ago
- A classifier for tumor microenvironment subtype based on ensemble machine learning models☆11Jul 20, 2025Updated last year
- Surface Marker Detection Using Single Cell Data☆13Apr 21, 2026Updated 6 months ago
- The Tomographer package implements the mathematical spatial image reconstruction of any set of read counts as described in the following …☆11May 15, 2021Updated 5 years ago
- Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data☆23May 19, 2025Updated last year
- An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data☆14Apr 1, 2018Updated 8 years ago
- Testing a neutral evolution model on cancer sequencing data☆10Feb 17, 2021Updated 5 years ago
- cTPnet Package☆28Jul 12, 2022Updated 4 years ago
- Trajectory Inference Based on SNP information.☆24Jun 19, 2024Updated 2 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Integrative Structural Variant analysis☆13May 9, 2023Updated 3 years ago
- ☆14Oct 14, 2022Updated 4 years ago
- ☆20Sep 5, 2023Updated 3 years ago
- Experimental source code for MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout)☆20Apr 27, 2015Updated 11 years ago
- A highly interactive single-cell bioinformatics workflow management library. Built with dataforest☆10Oct 4, 2022Updated 4 years ago
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆105Feb 11, 2026Updated 8 months ago
- Code related to scRNA analysis using the scAmpi workflow☆26Jun 24, 2026Updated 4 months ago
- Scripts for analyzing ATAC-STARR data.☆10Feb 5, 2024Updated 2 years ago
- A portable and fast single cell type identifier☆63May 12, 2021Updated 5 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Repository for Cibersortx☆63Mar 18, 2021Updated 5 years ago
- Clone identification from single-cell data☆67Nov 10, 2022Updated 3 years ago
- A public clone of the HypoMap Figure & analysis repository.☆12Sep 26, 2022Updated 4 years ago
- ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods☆13Jan 10, 2024Updated 2 years ago
- A web tool to do automatic spots detections and positional adjustments for Spatial Transcriptomics Datasets.☆26Nov 17, 2022Updated 3 years ago
- A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.☆16Jul 6, 2026Updated 3 months ago
- represent each cell in UMAP plots as a pie chart☆16Sep 27, 2021Updated 5 years ago
- Minimal scripts to reproduce the RADICL-seq analysis of the Nature Communications manuscript☆11Jan 30, 2020Updated 6 years ago
- code and dataset for spatialDWLS☆14Apr 18, 2021Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- 10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC☆30Mar 26, 2026Updated 7 months ago
- Spatial Transcriptomics Dashboard☆27Jul 6, 2023Updated 3 years ago
- Higher level repo for aggregating all of Atlas workflow logic for Single Cell☆14Jul 9, 2026Updated 3 months ago
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆27Aug 29, 2026Updated 2 months ago
- Cell cycle pseudotime in single-cell RNA-seq☆10Mar 31, 2025Updated last year
- Modeling of time series data for CRISPR KO experiments☆42Oct 1, 2026Updated 3 weeks ago
- LARIS maps ligand-receptor signalling in spatial transcriptomics within and across tissue states☆18Oct 13, 2026Updated 2 weeks ago