nf-core / imcytoLinks
Image Mass Cytometry analysis pipeline
☆26Updated 2 months ago
Alternatives and similar repositories for imcyto
Users that are interested in imcyto are comparing it to the libraries listed below
Sorting:
- Tools to handle IMC data☆23Updated 3 years ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆48Updated 3 years ago
- Histology Topography Cytometry Analysis Toolbox☆67Updated 2 years ago
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆15Updated 3 years ago
- ☆29Updated last year
- ☆38Updated last year
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆64Updated last month
- An R package for performing cell typing in SMI and other single cell data☆39Updated 3 months ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆114Updated this week
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆82Updated 3 weeks ago
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆21Updated last month
- ☆20Updated this week
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆36Updated last year
- Python package for Probe set selection for targeted spatial transcriptomics.☆40Updated last month
- Interactive applications of stlearn☆15Updated 2 years ago
- Identification of spatial homogeneous regions☆21Updated 7 months ago
- GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data☆59Updated 2 months ago
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆54Updated last month
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆27Updated last year
- Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…☆64Updated 9 months ago
- A web tool to do automatic spots detections and positional adjustments for Spatial Transcriptomics Datasets.☆24Updated 2 years ago
- The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…☆40Updated 3 months ago
- Bring your single-cell data to life☆88Updated last week
- Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…☆100Updated 4 months ago
- Spatially constrained color profiling for visualizing single-cell resolution spatial data☆26Updated 11 months ago
- Spatial Single-Cell Analysis Toolkit☆94Updated last month
- Segmentation error aware clustering for multiplexed imaging☆18Updated 7 months ago
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…☆66Updated last week
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆16Updated 3 months ago
- ☆44Updated last week