10xgenomics

rezakj/iCellR

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)).

10XGenomics/loupeR

Convert Seurat objects to 10x Genomics Loupe files.

bcgsc/arcs

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

LieberInstitute/spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app

LieberInstitute/HumanPilot

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

bcgsc/tigmint

⛓ Correct misassemblies using linked AND long reads

nf-core/spatialvi

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

wtsi-hpag/Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

lima1/sttkit

Pipeline for SpatialTranscriptomics and 10X Visium data

bcgsc/physlr

:chains: Construct a Physical Map from Linked Reads

epigen/scrnaseq_processing_seurat

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.

JDBLab/Pancreas_ductal_scRNAseq

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

quentinblampey/spatialdata_xenium_explorer

Interoperability between SpatialData and the Xenium Explorer

AlexsLemonade/scpca-nf

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

morispi/LRez

Standalone tool and library allowing to work with barcoded linked-reads

AllenInstitute/scrattch.io

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

kpatel427/multiome_analysis

Scripts for sincle cell multiome analysis

MargoKapustina/XeniumSpatialAnalysis

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

slowkow/saturation

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

bixBeta/TReX

RNA-seq, smRNA-seq, scRNA-seq & ATAC-seq workflows for @Cornell-Trex

morispi/LEVIATHAN

Linked-reads based structural variant caller with barcode indexing

nf-core/neutronstar

De novo assembly pipeline for 10X linked-reads using Supernova

metavannier/scRNAseq_analysis_workflow

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

OpenOmics/cyte-seek

Awesome single-cell CITE-sequencing Pipeline

deevdevil88/SN_Cortex_cell_atlas

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

LieberInstitute/visiumStitched

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/.

Meng0625/nCov

OpenOmics/cell-seek

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.

rnabioco/visium-probe-design

Generate probes for the 10x Genomics fixed assay

rusalkaguy/10x_genomics_tools

Scripts developed to work with 10x Genomics sequencing results

sjackman/tigmint-data

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

mostafa-ti/Master_thesis_bioinformatics

Repository of the master project in Bioinformatics at Lund University

Perik-Zavodskii/Visium-Deconvolution-based-clustering

Convert your STDeconvolve-generated and EnrichR-decoded topics into Seurat spatial clustering information via AUCell

Vincent-Therrien/easy-st

Tools that make spatial transciptomics easier / Outils pour simplifier la transcriptomique spatiale