A single-cell RNAseq pipeline for 10X genomics data
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Updated
Aug 21, 2024 - Nextflow
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
Convert Seurat objects to 10x Genomics Loupe files.
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.
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Pipeline for SpatialTranscriptomics and 10X Visium data
⛓️ 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
Interoperability between SpatialData and the Xenium Explorer
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.
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.
Scripts for sincle cell multiome analysis
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
🧽 Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.
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