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/.
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Updated
Oct 3, 2024 - R
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/.
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.
Code for the spatialLIBD R/Bioconductor package and shiny app
Convert Seurat objects to 10x Genomics Loupe files.
R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
Pipeline for SpatialTranscriptomics and 10X Visium data
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
Single-Cell RNA-seq analysis workflow 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)).
🧽 Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.
Scripts for sincle cell multiome analysis
Functions for handling RNA-seq files and formats as input and output for scrattch functions.
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
Rmarkdown scripts for adult human postmortem SN & Cortex cell atlas project.
Scripts developed to work with 10x Genomics sequencing results
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