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10x Genomics
Spatial Gene Expression

SPATIAL_RNA_COUNTER_CSCLOUPE_PREPROCESSCLOUPE_TILE_IMAGESSPACERANGER_PREFLIGHTSPACERANGER_PREFLIGHT_LOCALSPATIAL_IMAGING_CSALIGN_FIDUCIALSDETECT_TISSUEGPR_READERSTANDARDIZE_IMAGESSPATIAL_RNA_COUNTERPARSE_TARGET_FEATURESSPATIAL_REPORTERSPATIAL_RNA_ANALYZERANALYZER_PREFLIGHTCHOOSE_DIMENSION_REDUCTIONCHOOSE_DIMENSION_REDUCTION_OUTPUTCOMBINE_CLUSTERINGCORRECT_CHEMISTRY_BATCHMERGE_CLUSTERSPREPROCESS_MATRIXRUN_DIFFERENTIAL_EXPRESSIONRUN_FBPCARUN_GRAPH_CLUSTERINGRUN_KMEANSRUN_MULTIGENOME_ANALYSISRUN_PCARUN_TSNERUN_UMAPSUMMARIZE_ANALYSISWRITE_GENE_INDEX_BASIC_SPATIAL_RNA_COUNTERFILTER_BARCODESWRITE_POS_BAM_CELLS_REPORTERSUBSAMPLE_READSSUMMARIZE_BASIC_REPORTSWRITE_MOLECULE_INFO_MATRIX_COMPUTERALIGN_AND_COUNTBARCODE_CORRECTIONCOLLATE_METRICSMAKE_SHARDMERGE_METRICSSET_ALIGNER_SUBSAMPLE_RATEWRITE_BARCODE_SUMMARYWRITE_H5_MATRIXWRITE_MATRIX_MARKET_SLFE_PARTIAL_FIRST_PASSINITIAL_ALIGN_AND_COUNTSET_TARGETED_UMI_FILTERSUBSAMPLE_BARCODES_TARGETED_ANALYZERCALCULATE_TARGETED_METRICSSUBSAMPLE_OFF_TARGET_READSSUBSAMPLE_ON_TARGET_READSSUMMARIZE_TARGETED_ANALYSISSPATIAL_RNA_COUNTER_PREPCHEMISTRY_DETECTORMULTI_SETUP_CHUNKS
  SPATIAL_RNA_COUNTER_CS

This is the main Space Ranger pipeline that performs spatial RNA-seq analysis, spot alignment and tissue detection.