Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

Convert Seurat objects to 10x Genomics Loupe files.

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Code for the spatialLIBD R/Bioconductor package and shiny app

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

⛓ Correct misassemblies using linked AND long reads

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Pipeline for SpatialTranscriptomics and 10X Visium data

Interoperability between SpatialData and the Xenium Explorer

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

⛓️ Construct a Physical Map from Linked Reads

The following repository contains code for all scRNAseq analysis and visualization performed in the paper: Single cell resolution analysis of the human pancreatic ductal progenitor cell niche

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

Standalone tool and library allowing to work with barcoded linked-reads

Scripts for sincle cell multiome analysis

Functions for handling RNA-seq files and formats as input and output for scrattch functions.

R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients