A single-cell RNAseq pipeline for 10X genomics data
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Updated
May 22, 2024 - Nextflow
A single-cell RNAseq pipeline for 10X genomics data
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
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)).
Code for the spatialLIBD R/Bioconductor package and shiny app
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
⛓ 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.
Convert Seurat objects to 10x Genomics Loupe files.
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
Scripts for sincle cell multiome analysis
De novo assembly pipeline for 10X linked-reads using Supernova
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Standalone tool and library allowing to work with barcoded linked-reads
Functions for handling RNA-seq files and formats as input and output for scrattch functions.
Single-cell/nuclei pipeline for data derived from Oxford Nanopore
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
Linked-reads based structural variant caller with barcode indexing
R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
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