10xgenomics

There are 2 repositories under 10xgenomics topic.

• nf-core / scrnaseq

  A single-cell RNAseq pipeline for 10X genomics data

  nf-corenextflowworkflowpipeline10x-genomics10xgenomicsalevinbustoolscellrangerkallistorna-seqsingle-cellstar-solo
  Language:Nextflow 168

• 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)).

  singel-cell-sequencingclustering-algorithmclusteringnormalizationumappseudotimescrna-seqscvdj-seqcite-seq3dintractive-graph10xgenomicsdropoutbatch-normalizationimputationdiffusion-mapscell-type-classificationicellr
  Language:R 116

• bcgsc / arcs

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

  c-plus-plussciencebioinformaticsassemblerscaffoldgenome10xgenomicsgraphnanopore-sequencingoxford-nanoporepacbio-data
  Language:C++ 90

• LieberInstitute / spatialLIBD

  Code for the spatialLIBD R/Bioconductor package and shiny app

  rstatsshinyspatial-transcriptomics10xgenomicsbioconductorgolemvisiumspatialexperiment
  Language:R 68

• 10XGenomics / loupeR

  Convert Seurat objects to 10x Genomics Loupe files.

  10xgenomicsr-packagesingle-cell-genomics
  Language:R 64

• LieberInstitute / HumanPilot

  Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

  spatial-transcriptomicsrstats10xgenomicsvisiumdlpfchumanbrainanalysisbiorxiv
  Language:HTML 59

• bcgsc / tigmint

  ⛓ Correct misassemblies using linked AND long reads

  misassembly-correctiongenome-scaffoldinggenome-assemblylinked-reads10xgenomicsbioinformaticsbioinformatics-tool
  Language:Python 54

• nf-core / spatialtranscriptomics

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

  nf-corenextflowworkflowpipeline10x-genomics10xgenomicsbioinformaticsimage-processingmicroscopyrna-seqsingle-cellspatialspatial-transcriptomicssttranscriptomicsvisium
  Language:Nextflow 38

• wtsi-hpag / Scaff10X

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

  genomicsgenomeassembly10xgenomicsscaffoldingbreakingbioinformatics
  Language:C 20

• lima1 / sttkit

  Pipeline for SpatialTranscriptomics and 10X Visium data

  visium10xgenomicsspatial-transcriptomics
  Language:R 19

• bcgsc / physlr

  :chains: Construct a Physical Map from Linked Reads

  genome-assemblygenome-scaffoldinglinked-reads10xgenomicsbioinformaticsbioinformatics-tool
  Language:Python 15

• 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

  scrna-seq-analysispancreas10xgenomics
  Language:R 15

• morispi / LRez

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

  barcodebarcodeslinked-readslinkedreads10x10xgenomics10x-genomicsindexhaplotaggingtell-seqstlfrbioinformatics
  Language:C++ 12

• AlexsLemonade / scpca-nf

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

  10xgenomicsalevin-frynextflowrna-seq-quantificationscrna-seqcite-seqspatial-transcriptomics
  Language:R 11

• AllenInstitute / scrattch.io

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

  transcriptomicsrtomeloom10xgenomicshdf5
  Language:R 10

• kpatel427 / multiome_analysis

  Scripts for sincle cell multiome analysis

  seuratsingle-cell10xgenomicsseurat-objectssingle-cell-rna-seqsingle-cell-analysissingle-cell-atac-seq
  Language:R 9

• quentinblampey / spatialdata_xenium_explorer

  Converting any SpatialData object into files that can be open by the Xenium Explorer

  10xgenomicsspatial-analysisspatial-omicsspatialdatavisualization
  Language:Python 9

• epigen / scrnaseq_processing_seurat

  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.

  bioinformaticsworkflowsnakemakescrna-seqbiomedical-data-sciencecite-seqsccrispr-seq10xgenomicssnrna-seqsingle-cellvisualization
  Language:R 6

• bixBeta / TReX

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

  10xgenomicsrnaseqsinglecellscrnashiny-appsshinybash-scriptbash-scriptingsmallrna-seqsmallrnamirdeep2starseuratmultiqcggplot2
  Language:Shell 4

• morispi / LEVIATHAN

  Linked-reads based structural variant caller with barcode indexing

  linked-readsbarcodesstructural-variationsvs10xgenomics
  Language:C++ 4
• neutronstar

  nf-core / neutronstar

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

  denovo-assemblygenome-assemblylinked-readsnf-corenextflowworkflowpipeline10xgenomics10x-genomicssupernova
  Language:Nextflow 4

• slowkow / saturation

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

  10xgenomicsbioinformaticsgene-expressionngs-analysisvdj
  Language:R 3

• OpenOmics / cyte-seek

  Awesome single-cell CITE-sequencing Pipeline

  pipelinesingularitysingle-cellcite-seqquality-control10xgenomics
  Language:Python 2

• deevdevil88 / SN_Cortex_cell_atlas

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

  10xgenomicssingle-nuclei-rna-sequencingcell-atlasparkinsons-diseaseneurodegenerative-diseasesmagmaldscore
  Language:R 1

• Meng0625 / nCov

  covid-19covid-19-data-analysisscrna-seq10xgenomics
  Language:HTML 1

• metavannier / scRNAseq_analysis_workflow

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

  bioinformaticssc-rna-seqseurat10xgenomicssnakemakedifferential-expression
  Language:R 1

• nf-core / scnanoseq

  Single-cell/nuclei pipeline for data derived from Oxford Nanopore

  10xgenomicslong-read-sequencingnanoporenextflownf-corescrna-seqsingle-cell
  Language:Nextflow 1

• 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.

  single-cell-atac-seqsingle-cell-omicssingle-cell-rna-seq10xgenomicssingle-cell-vdjsingle-cell-cite-seq
  Language:Python 1

• rnabioco / visium-probe-design

  Generate probes for the 10x Genomics fixed assay

  10xgenomicsrna-seq
  Language:Python 1

• rusalkaguy / 10x_genomics_tools

  Scripts developed to work with 10x Genomics sequencing results

  r10xgenomics10x10x-genomicsloupe
  Language:R 1

• sjackman / tigmint-data

  Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

  misassembly-correctiongenome-scaffoldinggenome-assemblylinked-reads10xgenomicsbioinformaticsbioinformatics-analysis
  Language:Makefile 1

• csawye01 / nf-core-demultiplex

  Demultiplexing pipeline for sequencing data

  nf-corenextflownextflow-pipelinesdemultiplexingfastqcbcl2fastq10xgenomicssinglecell
  Language:Nextflow 0

• MargoKapustina / XeniumSpatialAnalysis

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

  10xgenomicsspatial-transcriptomicsspatial-data-analysisxenium
  Language:R 0

• mostafa-ti / Master_thesis_bioinformatics

  Repository of the master project in Bioinformatics at Lund University

  single-cell-rna-sequencingvelocity-analysiscellrangerscanpyscvelo10xgenomicsvelocyto
  Language:Jupyter Notebook 0

• biopet / 10xkit

  10xgenomics
  Language:Scala

• Vincent-Therrien / easy-st

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

  10xgenomicspythonspatialtranscriptomics
  Language:Jupyter Notebook