nf-core / mcmicroLinks
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
☆15Updated last month
Alternatives and similar repositories for mcmicro
Users that are interested in mcmicro are comparing it to the libraries listed below
Sorting:
- A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)☆12Updated last month
- ☆19Updated 2 weeks ago
- ☆29Updated last year
- ☆27Updated 7 months ago
- Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…☆27Updated this week
- R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…☆14Updated 3 years ago
- A scalable machine learning pipeline for probe specificity prediction.☆14Updated last year
- Identification of spatial homogeneous regions☆21Updated 4 months ago
- Image Mass Cytometry analysis pipeline☆25Updated last month
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆62Updated 2 weeks ago
- ☆17Updated last week
- Segmentation error aware clustering for multiplexed imaging☆18Updated 4 months ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆37Updated last year
- Python package for Probe set selection for targeted spatial transcriptomics.☆37Updated 6 months ago
- Probabilistic cell segmentation for in situ spatial transcriptomics☆90Updated this week
- https://sparrow-pipeline.readthedocs.io/en/latest/☆27Updated last week
- Single-cell spatial proteomics analysis that makes you happy!☆28Updated this week
- Slides and Notebooks for scverse 2024☆17Updated 8 months ago
- The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.☆27Updated 8 months ago
- Tools to handle IMC data☆23Updated 3 years ago
- Pipeline for designing custom probes against human genes☆16Updated 6 months ago
- An R package for performing cell typing in SMI and other single cell data☆37Updated 2 weeks ago
- An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.☆14Updated last year
- ☆53Updated this week
- Automatically annotate cell types, consistently across samples.☆13Updated last month
- Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.☆11Updated last month
- A Python toolkit for subcellular analysis of spatial transcriptomics data☆79Updated 2 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆46Updated this week
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆54Updated this week
- ☆28Updated 7 months ago