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List of tools

The following tools use BAM files as input. These BAM files could come from any single-cell genomics protocol, as long as they have a tag that specifies the cell barcodes.

.. toctree::
    :maxdepth: 1

    tools/scFilterBarcodes
    tools/scFilterStats
    tools/scCountReads
    tools/scBulkCoverage
    tools/scJSD

The following tools use the scloom output produced within the sincei analysis workflow. The format of scloom file is same as .loom, but it contains extra metadata that's needed for sincei tools.

.. toctree::
    :maxdepth: 1

    tools/scCountQC
    tools/scCombineCounts
    tools/scClusterCells
    tools/scPlotRegion
tool type input files main output file(s) application
:ref:`scFilterBarcodes` preprocessing BAM/SAM files text file with filtered cell barcodes Identify and filter cell barcodes (for droplet-based single-cell seq)
:ref:`scFilterStats` QC BAM/SAM files text file with QC per cell Produce per-cell statistics after filtering reads by user-defined criteria.
:ref:`scCountReads` preprocessing BAM/SAM files scloom object with cellxregion counts Counts reads for each barcode on genomic bins or user-defined features.
:ref:`scCountQC` QC scloom object QC metrics / filtered scloom file Perform quality control and filter the output of scCountReads.
:ref:`scCombineCounts` preprocessing scloom objects merged scloom object Concatenate/merge the counts from different samples/batches or modalities
:ref:`scClusterCells` analysis scloom object .tsv file with clusters, png with UMAP Perform dimensionality reduction and clustering on the output of scCountReads.
:ref:`scBulkCoverage` analysis tsv file + BAM file bigwig files Get pseudo-bulk coverage per group using a user-supplied cell->group mapping (output of scClusterCells).