Stars
Repository for ENACT pipeline for end-to-end analysis of Visium HD data
Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing
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A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
rapids-singlecell: GPU-accelerated framework for scRNA analysis
A pipeline for processing single-cell and spatial long-read transcriptomic data
Track Nextflow strict syntax linting health across nf-core pipelines
gerstung-lab / segger
Forked from EliHei2/segger_deva cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex ima…
Spatial transcriptomics analyses and decoding in R
marker-based purification of cell types from single-cell RNA-seq datasets
R package with well defined templates for most common pipelines
nf-neuro is a nextflow neuroimaging library maintained by the SCIL team
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
An interactive explorer for single-cell transcriptomics data
Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue"
Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Bayesian Segmentation of Spatial Transcriptomics Data
scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions