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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_COUNTERSPATIAL_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_ANALYSIS_BASIC_SPATIAL_RNA_COUNTERALIGN_READSATTACH_BCS_AND_UMISBUCKET_BY_BCCHUNK_READSCOUNT_GENESEXTRACT_READSFILTER_BARCODESMARK_DUPLICATESREPORT_MOLECULESSORT_BY_BCSORT_BY_POSSUBSAMPLE_READSSUMMARIZE_BASIC_REPORTSSUMMARIZE_READ_REPORTSSPATIAL_RNA_COUNTER_PREPCHEMISTRY_DETECTORDETECT_CHEMISTRYSETUP_CHUNKS
  SPATIAL_RNA_COUNTER_CS

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