10xgenomics

Convert Seurat objects to 10x Genomics Loupe files.

iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. It supports a variety of single-cell technologies, including scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq, and Spatial Transcriptomics (ST).

Code for the spatialLIBD R/Bioconductor package and shiny app

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.

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

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

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

Scripts for sincle cell multiome analysis

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

🧽 Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.

R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.

comprehensive reproducible benchmarking framework for single-cell and spatial long-read transcriptomics

Official scRNA-seq workshop – El Arkhe MultiOmics

Single-Cell RNA-seq analysis workflow for 10x Genomics data

Scripts developed to work with 10x Genomics sequencing results

Rmarkdown scripts for adult human postmortem SN & Cortex cell atlas project.

scRNA seq analysis of mouse brain data from 10x genomics platform.