Pipeline for SpatialTranscriptomics and 10X Visium data
☆22Jul 22, 2025Updated 10 months ago
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:
- Code required to reproduce analysis of the single cell Cut and Tag data in the resource paper (Bartosovic et. al., 2020)☆14Apr 2, 2026Updated 2 months ago
- Spatial transcriptomics of heart tissue☆111Oct 7, 2023Updated 2 years ago
- scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data☆32Dec 22, 2022Updated 3 years 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
- ☆17Sep 16, 2024Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data☆14Apr 1, 2018Updated 8 years ago
- Splotch is a hierarchical generative probabilistic model for analyzing Spatial Transcriptomics (ST) data☆21May 19, 2025Updated last year
- A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.☆16Jan 15, 2024Updated 2 years ago
- Repository for Cibersortx☆62Mar 18, 2021Updated 5 years ago
- A public clone of the HypoMap Figure & analysis repository.☆11Sep 26, 2022Updated 3 years ago
- Trajectory Inference Based on SNP information.☆24Jun 19, 2024Updated last year
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆99Feb 11, 2026Updated 4 months ago
- Higher level repo for aggregating all of Atlas workflow logic for Single Cell☆14Mar 31, 2026Updated 2 months ago
- represent each cell in UMAP plots as a pie chart☆16Sep 27, 2021Updated 4 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.
- Minimal scripts to reproduce the RADICL-seq analysis of the Nature Communications manuscript☆11Jan 30, 2020Updated 6 years ago
- Experimental source code for MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout)☆20Apr 27, 2015Updated 11 years ago
- Spatial Transcriptomics Dashboard☆27Jul 6, 2023Updated 2 years ago
- A highly interactive single-cell bioinformatics workflow management library. Built with dataforest☆10Oct 4, 2022Updated 3 years ago
- Analysis of Single Cell Expression, Normalization and Differential expression☆14Feb 29, 2020Updated 6 years ago
- SciLifeLab SIB Summer School for Advanced topics in Single Cell Omics. Site: https://nbisweden.github.io/single-cell_sib_scilifelab_2021/☆23Sep 19, 2021Updated 4 years ago
- Annotation and Prediction of Oncogenic Gene Fusions in RNAseq☆12Feb 20, 2016Updated 10 years ago
- Code and data repository for the 2020 physalia course on single cell RNA sequencing.☆59Apr 15, 2020Updated 6 years ago
- Analytical pipeline developed to anlayze Cut and Run data. Inspired by both Henikoff (SEACR) and Orkin (Cut&RunTools) lab pipelines.☆20May 26, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations☆32May 12, 2020Updated 6 years ago
- ☆21Dec 23, 2024Updated last year
- This is the official repository for the Human Cell Atlas Heart project.☆32Jul 28, 2020Updated 5 years ago
- This is the repository which contains the code that was used to generate the results and figures of the “Single-cell RNA-sequencing revea…☆13Apr 14, 2026Updated last month
- Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).☆49Feb 9, 2024Updated 2 years ago
- Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project☆97Mar 26, 2026Updated 2 months ago
- iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. …☆128Nov 10, 2025Updated 7 months ago
- single cell sequencing analysis tutorial☆18Jan 15, 2020Updated 6 years ago
- A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learn…☆11May 19, 2021Updated 5 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Create NNN primers tiling codons of a gene for codon mutagenesis☆14Jan 13, 2021Updated 5 years ago
- A framework around Tensorflow-Keras that makes it easy to train and evaluate any deep learning architecture on imaging flow cytometry dat…☆12Dec 8, 2022Updated 3 years ago
- Repository for ENACT pipeline for end-to-end analysis of Visium HD data☆81Feb 10, 2026Updated 4 months ago
- ☆32Jun 12, 2020Updated 5 years ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆61Aug 17, 2024Updated last year
- Bostongene cell deconvolution algorithm from RNAseq☆60Jan 15, 2024Updated 2 years ago
- Code related to scRNA analysis using the scAmpi workflow☆28Jan 21, 2026Updated 4 months ago