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Change Log

version 1.6.0

Changes

  • enrichment_vectorized has been re-written such that the pseudocount is only applied to the background in a given promoter region.
  • poisson_pvalue has been re-written to remove the pseudocount from the experiment_hops in the promoter regions
  • adding a significant amount of error handling and input/output validity checks to the metric calculations in yeast Peak Calling
    1. chrmap nrow must be > 0 and ncol > 1
    2. background data (hops) must have at least one hop. Will error if not.
    3. experiment data (hops) must have at least one hop. Will error if not.
    4. promoter set files must have at least 1 promoter region
    5. enrichment input and output is checked for type expectations
  • Old un-vectorized enrichment, poisson and hypergeometric code files removed

#Version 1.5.2

Changes

  • added kwargs arguments to PeakCalling.yeast.call_peaks to allow user to pass in validation method on pyranges join, background_total_hops and experiment_total_hops.
  • moved promoters_df to promoters_pr conversion in PealCalling.yeast.call_peaks from call_peaks to external function. Also corrected the slack in the join method where the overlaps are counted. Now in the conversion method, the End is incremented by 1 to allow hops on the right endpoint, whatever that is, to be counted.

Version 1.5.1

Changes

  • Needed to keep name in the output of PeakCalling.yeast.call_peaks
  • adding Analysis and PeakCalling modules to the documentation API section

Version 1.5.0

Changes

  • overhaul of the PeakCalling/yeast module to address memory usage. adding pyranges as a depedency as a result. removed consider_strand and added a argument to deduplicate the experiment qbeds based on chr, start, end

Version 1.4.1

Changes

  • chipexo_promoter_sig now checks the columns and expects the original yeastepigenome.org allevents coord column to be split into start and end where end is simply coord + 1. This is to be consistent with the other bed-type files.

Version 1.4.0

Additions

For yeast, changing the yeast_call_peaks consider_strand functionality to collapse read counts at the same coordinate on the forward/reverse strand in addition to ignoring the strand with regards to the promoter.

Version 1.3.0

Additions

For yeast, adding peak calling and analysis functionality. This includes the following to the cmd line: - yeast_call_peaks - call peaks on a yeast qBED file - yeast_chipexo_promoter_sig - calculate the significance of the promoter signal over a given set of promoter regions - yeast_rank_response - Given a promoter set and expression data, compare the binding and expression sets

Changes

  • the yeast barcode qc summary outputs the actual r1/r2 sequences as opposed to just the edit distance equivalent classes

Version 1.2.0

Bug fixes

  • Removing the deprecated (and removed in pandas 2.0) DataFrame.append function calls from Qbed.py

Version 1.1.0

Bug fixes

  • Adding SRT annotation to mammals qBED output

Features/not bugs

  • Remove header from mammals qBed
  • Fix typo in mammals barcode details – the component identified with lrt should be (and now is) ltr

Version 1.0.0

  • Initial release