RnaChipIntegrator-v3.0.0

• Add option to compute distances from gene TES only (--edge=tes) (PR #77).
• Add CITATION.cff file and update information on how to cite RnaChipIntegrator (PR #78).
• Update the installation documentation and metadata (PR #85, PR #86).
• Add automated CI testing and deployment to PyPI via GitHub Actions, and add support for Python 3.9 (PR #74).
• Drop support for Python 2.7 (PR #76).

RnaChipIntegrator-v2.0.0

• Add support for Python 3 (3.5, 3.6, 3.7 and 3.8) (PR #69, PR #71).

RnaChipIntegrator-v1.2.0

• Implement batch mode operation which allows a single run of RnaChipIntegrator to iterate over any
  combination of multiple cutoffs (via new --cutoffs option) and multiple peaks and genes files (via new
  --peaks and --genes options) (PR #58).
• Drop support for Python 2.6 (PR #66).

RnaChipIntegrator-v1.1.0

• Fix bug in gene-centric analysis when using --edge=both, which meant valid peaks could sometimes be dropped from the results (PR #60)
• New --peak_id option enables peak names to be read from an ID column in the peaks file, which will be carried through to the output files (PR #56)
• New --analyses option enables specific analyses to be selected (i.e. either peak-centric only, gene-centric only, or both peak- and gene-centric) (PR #46)

RnaChipIntegrator-v1.0.3

• Update description of direction in the documentation and the XLSX file, to clarify the meaning of the terms upstream and downstream in the program outputs.
• Update documentation to explain how comments, header lines, and lines with 'bad' data, are handled by the program when reading in the input files.
• Add a section on 'known problems' to the documentation.

RnaChipIntegrator-v1.0.2

Bugfix release: fixes bug which crashed the program if --cutoff=0 was specified together with --xlsx.

RnaChipIntegrator-v1.0.1

Bugfix release: fixes a bug which crashed the program if --cutoff=0 was specified.

RnaChipIntegrator-v1.0.0

Complete rewrite of RnaChipIntegrator to simplify installation and usage, and unify internal algorithms alongside substantial updates to the documentation.

Significant changes include:

• Usage:
  • no distinction is now made between 'summits' and 'peaks'; the same algorithm is applied in each case.
  • the program always finds the nearest genes to each peak, and vice versa. The same distance cutoff and maximum number of hits are applied to both and can be specified using the --cutoff and --number options.
  • by default nearest distances between peaks and gene are calculated from the TSS of the gene to whichever of the peak edges are closer; alternatively distances can be calculated between the nearest pair of peak/gene edges by specifying the --edge=both option.
  • any differential expression flags in the input genes file are ignored unless the --only-DE option is specified, in which case only the differentially expressed genes are considered in the analyses.
  • arbitrary columns from input peaks file can be specified using --peak_cols options to set chromosome, start and end.
• Output:
  • by default all pairs within the cut-off distance are reported unless the user explicitly restricts this to a subset by specifying the --number option (i.e. --number now turned off by default).
  • by default each peak/gene pair is reported on a separate line; the --compact option reports all nearest gene/peaks on a single line of output.
  • new direction field in output indicates whether hits are up- or downstream from reference.
  • output file names now end with 'gene-centric' and 'peak-centric'.
  • Excel output is only produced if the --xlsx option is specified; spreadsheets are now output in XLSX format (instead of XLS).
  • summary output is only produced if --summary is specified.
• Installation:
  • installs using pip and can be obtained directly from PyPI using pip install RnaChipIntegrator
  • executable now installs as RnaChipIntegrator (i.e. no .py extension)
  • the rearrange_columns.py utility has been dropped.
• Documentation:
  • full documentation now available via ReadTheDocs at http://rnachipintegrator.readthedocs.org/en/latest/

RnaChipIntegrator-v0.5.0-alpha.8

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.7:

• Fix typo in XLSX 'notes' sheet.

RnaChipIntegrator-v0.5.0-alpha.7

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.6:

• Update --xls option to --xlsx and generate XLSX files (instead of XLS); as XLSX has much greater limits on the number of rows and columns allowed in a worksheet this should address previous problems with having data split over multiple sheets.
• Correct headers and placeholders now output when using --compact option when --number is not specified.
• Pre-existing output files are explicitly removed before analysis is run (rather than relying on overwrite).