NEWS

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PIPETS 1.1.5 (2024-09-27)

• Added strand specific analysis parameters. Can now use different threshAdjust and highOutlierTrim values for each strand should they choose.

PIPETS 1.1.4 (2024-09-11)

• Resolved warnings that popped up during Initial Poisson Distribution testing. Results will not be greatly changed but now PIPETS correctly counts all reads.
• Fixed problems in Genomic Ranges input method so that it now correctly mirrors the analysis performed for bed file inputs.

PIPETS 1.1.3 (2024-07-12)

• Changed read quality score parameter from a set value to a minimum, so anything equal to or greater than the input value will be considered

PIPETS 1.1.2 (2024-07-11)

• Changed PIPETS to use read quality score as a cutoff instead of read length. Functions as better trimming process
• Input bed files and GRanges objects now both correctly use read quality score
• Updated Vignette file wording to properly match recent changes

PIPETS 1.1.1 (2024-06-06)

• Resolved Git inconsistencies, made minor fixes

PIPETS 1.1.0 (2024-05-14)

• Added Benjamini-Hochberg multiple testing correction to help reduce incidence of Type I error

PIPETS 1.0.0 (2024-02-20)

• Accepted to Bioconductor
• Accepts both bedFile and GRanges as input formats
• Outputs strand-split bed files and strand-split output files containing identified significant 3'-end peaks for both input formats