Pipelines

• pipeline_adt_norm.py
  • Overview
  • Pipeline output
  • Code
• gexdepth()
• gexdepthAPI()
• adtdepth()
• adtdepthAPI()
• adt_plot_norm()
• dsb_norm()
• dsbAPI()
• median_norm()
• medianAPI()
• clr_norm()
• clrAPI()
• plot()
• full()
• pipeline_ambient_rna.py
  • Overview
  • Pipeline output
  • Code
• ambient_rna_per_input()
• ambient_rna_compare()
• plot()
• full()
• pipeline_annotation.py
  • Overview
  • Usage
  • Pipeline output
• fetchEnsembl()
• ensemblAPI()
• fetchKegg()
• keggAPI()
• pipeline_cellbender.py
  • Overview
  • Pipeline output
  • Code
• cellbender()
• h5API()
• mtx()
• mtxAPI()
• full()
• useCounts()
• pipeline_celldb.py
  • Overview
  • Code
• connect()
• load_samples()
• load_gex_qcmetrics()
• load_gex_scrublet()
• load_singleR()
• load_gmm_demux()
• load_demuxEM()
• load_souporcell()
• final()
• pipeline_cellranger.py
  • Overview
  • Usage
  • Code
• count()
• mtxAPI()
• h5API()
• tcr()
• registerTCR()
• mergeTCR()
• registerMergedTCR()
• bcr()
• registerBCR()
• mergeBCR()
• registerMergedBCR()
• full()
• useCounts()
• pipeline_cell_qc.py
  • Overview
  • Code
• qcmetrics()
• qcmetricsAPI()
• scrublet()
• scrubletAPI()
• plot()
• full()
• pipeline_cluster.py
  • Overview
  • Usage
  • Pipeline output
  • Code
• taskSummary()
• preflight()
• metadata()
• loom()
• neighbourGraph()
• scanpyCluster()
• cluster()
• compareClusters()
• clustree()
• paga()
• UMAP()
• plotRdimsFactors()
• plotRdimsClusters()
• plotRdimsSingleR()
• plotSingleR()
• summariseSingleR()
• plotGroupNumbers()
• clusterStats()
• findMarkers()
• summariseMarkers()
• topMarkerHeatmap()
• dePlots()
• markerPlots()
• plotMarkerNumbers()
• markers()
• parseGMTs()
• genesetAnalysis()
• summariseGenesetAnalysis()
• genesets()
• plots()
• latexVars()
• summaryReportSource()
• summaryReport()
• markerReportSource()
• markerReport()
• export()
• report()
• cellxgene()
• pipeline_dehash.py
  • Overview
  • Usage
  • Code
• gmmDemux()
• gmmAPI()
• hashCountCSV()
• demuxEM()
• parseDemuxEM()
• demuxemAPI()
• pipeline_emptydrops.py
  • Overview
  • Usage
  • Pipeline output
  • Code
• emptyDrops()
• meanReads()
• full()
• pipeline_fetch_cells.py
  • Overview
  • Usage
  • Pipeline output
• fetchCells()
• fetchCounts()
• pipeline_singleR.py
  • Overview
  • Usage
  • Pipeline output
  • Code
• genSingleRjobs()
• singleR()
• concatenate()
• summary()
• singleRAPI()
• pipeline_velocyto.py
  • Overview
  • Usage
  • Pipeline output
  • Code
• checkInputs()
• genClusterJobs()
• sortBam()
• runVelocyto()
• full()