scATAC-pro_V1.2.0

• updated footprint dependency rgt-hint module to python3
• saved QC statistics in html report into tables, and peak added calling summary information in the report
• added QC per cell to seurat obj metadata as: total.unique.frags, frac.peak, frac.mito,
  frac.tss, frac.promoter, and frac.enhancer

scATAC-pro_V1.1.4

• Accept input for process and demplx_fastq as folder path of 10x fastq files (per sample).
• Other minor corrections

scATAC-pro_V1.1.3

note:

• for runGO module, update background genes as genes associated with any peak
• other minor changes

scATAC-pro_V1.1.2

V1.1.2, updates includes:

• integrate: add VFACS (Variable Features Across ClusterS) option for the integration module,
  which reselect variable features across cell clusters after an initial clustering, followed by
  another round of dimension reduction and clustering, specify Integrate_by = VFACS in configure file
• clustering: filter peaks before clustering (accessible in less than 0.5% of cells) and
  remove rare peaks (accessible in less than 1% of cells) from the variable features list
• reConsMtx: enable specifying a path for saving reconstructed matrix (optional)

scATAC-pro_V1.1.1

Minor updates such as:

1. The get_mtx module requires two input files: a fragments.txt file and a peak file, separated by comma
2. Annotate peak as overlapped with a gene Tss if the corresponding distance <= 1000bp; and mark peak associated with a gene if their distance <= 100kb

scATAC-pro_V1.1.0

Release of scATAC-pro v1.1.0.

scATAC-pro_V1.0.1

Updates:

1. correct few minor bugs for generating summary reports
2. install additional packages in dockerized version

scATAC-pro_V1.0.0

scATAC-pro_v1.0.0

add more qc for cell barcodes