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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
CLI platform to experiment with codegen. Precursor to: https://lovable.dev
Examples of single-cell genomic analysis accelerated with RAPIDS
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Collections of library structure and sequence of popular single cell genomic methods
A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.
Source code to the Ratlas Shiny app - making science accessible and searchable
💡 Easily improve the user experience of your Shiny apps in seconds
Docker Containers for Bioconductor
Run current & prior versions of R using docker. rocker/r-ver, rocker/rstudio, rocker/shiny, rocker/tidyverse, and so on.
Python package with helper tools for the nf-core community.