A single-cell RNAseq pipeline for 10X genomics data

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)).

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

Code for the spatialLIBD R/Bioconductor package and shiny app

Convert Seurat objects to 10x Genomics Loupe files.

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.

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

Pipeline for SpatialTranscriptomics and 10X Visium data

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

⛓️ Construct a Physical Map from Linked Reads

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

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

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

Converting any SpatialData object into files that can be open by the Xenium Explorer

Scripts for sincle cell multiome analysis

A Snakemake workflow 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.

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

De novo assembly pipeline for 10X linked-reads using Supernova