Sixth release of PARE (v0.06)

• now allows one or more replicates
• number of processors can be specified
• also checks for bedtools, samtools and macs2 version

Fifth release of PARE (v0.05)

• bug fix; some shell versions do not support using "&>>", instead using "2&1" now (Thanks to Carlos Guzman for reporting the error)

Fourth release of PARE (v0.04)

• added -extsize parameter as required for latest release of MACS2

Third release of PARE (v0.03)

• contains changes in blockbuster_threshold_nfr.R script in order to produce more comprehensible output pdf file
• bug fix to create reproducible random regions (seed parameter of bedtools was missing at one place) - it was leading to few inconsistent results.

Second release of PARE (v0.02)

• bug fix while sorting genomic regions by coordinates (now using sort -k instead of sortBed) - it was leading to few inconsistent results.
• now using top 20,000 regions from Macs2 in place of all regions to more robustly compute block threshold parameter.

First release of PARE (v0.01)

This is the first release of PARE