Code for the spatialLIBD R/Bioconductor package and shiny app
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Updated
Jul 3, 2024 - R
Code for the spatialLIBD R/Bioconductor package and shiny app
R package containing functions useful for stitching Visium capture areas. Related to https://github.com/LieberInstitute/LS_visiumStitched
Interoperability between SpatialData and the Xenium Explorer
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
A single-cell RNAseq pipeline for 10X genomics data
Convert Seurat objects to 10x Genomics Loupe files.
R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients
Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Pipeline for SpatialTranscriptomics and 10X Visium data
Tools that make spatial transciptomics easier / Outils pour simplifier la transcriptomique spatiale
One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.
⛓️ Construct a Physical Map from Linked Reads
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)).
RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @cornell-TREX
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
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.
⛓ Correct misassemblies using linked AND long reads
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