scATAC-pro_v1.5.1

• integrate module takes SampleSheet.csv file as input, where sample names, paths of peaks, fragments, and cell barcodes can be specified
• Enable 4/5 bp shift for each read by setting SHIFT_READS_IN_BAM as TRUE in configure_user.txt file
• Correctted an error for processing single-end sequencing data in the mapping module

scATAC-pro_v1.5.0

• Donot annotate peaks in the seurat object (peaks are still annotated for modules runDA, runGO and visualize)
• Add new module process_from_align to do processing from alignment step (including aligment), given trimmed demultiplexed fastq files
• Enable to change default expected doublet rate in the configure_user.txt file
• Enable filtering peaks by qvalue in mergePeaks and integrate modules.

scATAC-pro_v1.4.4

• Only consider standard chromosomes in the qc_per_barcode module
• Correct a minor bug in the qc_per_barcode module
• Add version# in the html report
• Clean and correct a minor bug in the trimming module

scATAC-pro_v1.4.3

• Added a new module reprocess_cellranger_output to reprocess scATAC-seq data originally processed by cellranger
• Optimized some steps in mapping_qc module

scATAC-pro_v1.4.2

• corrected bugs in processing single-end sequencing data
• corrected minor underestimate of the overall FrIP in the html report file
• corrected a bug in process_with_bam module
• corrected a bug in integrate module

scATAC-pro_v1.4.1

• correct a bug relate to input filepath for report module
• record input file paths for the integration module
• using BAMPE for macs2 for paired-end sequencing
• update tutorial

scATAC-pro_v1.4.0

• labelTransfer: new module added, to do label trasfer (for cell annotation) from cell annotation of scRNA-seq data. First construct a gene by cell activity matrix, then use FindTransferAnchors and TransferData function from Seurat R package to predicted cell type annotation from the cell annotaiton in scRNA-seq data.

scATAC-pro_V1.3.1

• rmDoublets: new module added, to remove potential doublets using DoubletFinder algorithm.

scATAC-pro_v1.3.0

• qc_per_barcode: add tss enrichment score per cell into the QC metrics
• call_cell: enable filtering barcodes with minimal tss enrichment score cutoff (parameter min_tss_escore in the updated configure_user.txt file)
• fragments file indexed by tabix (named fragments.tsv.gz)
• footprint module: suppoort comparison of any two sets of cell clusters
• motif_analysis and runDA: enable seurat/matrix object in .rds format as input
• integrate: rename cell name for each sample to avoid shared barcodes among samples; enable a distance parameter to merge peaks
• integrate_mtx: new module added, as an alias of previous integrate_seu module

scATAC-pro_v1.2.1

• .rds files generated for matrices and can be inputs for clustering, motif_analysis and downstream modules
• added 'addCB2bam' module to write cell barcode into an additional column of the bam file & corrected a bug for calculating insert size