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.

• scFilterBarcodes
• scFilterStats
• scCountReads
• scBulkCoverage
• 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.

• scCountQC
• scCombineCounts
• scClusterCells
• scPlotRegion

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