RnaChipIntegrator-v0.5.0-alpha.6

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.5:

• Fix broken --xls option (crashed the program if specified)

RnaChipIntegrator-v0.5.0-alpha.5

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.4:

• Rename 'feature' to 'gene' in program output, documentation etc (this doesn't affect the program function)
• 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)
• Output file names changed to 'feature-centric' and 'peak-centric'
• Options are grouped into subsets when displayed by -h/--help
• Parameter defaults are also given in the documentation.
• Peaks in the input with start and end positions which aren't at least 1bp apart cause the program to raise an error.

RnaChipIntegrator-v0.5.0-alpha.4

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.3:

• Fix the broken --promoter_region option which was being ignored.

RnaChipIntegrator-v0.5.0-alpha.3

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.2:

• --compact now only changes the output format from "multi-line" (i.e. one hit pair per line) to "single-line" (i.e. all hits on the same line). The same fields are reported in both modes.
• The explanatory text for the dist_closest field has been updated to make it clearer what this means.

RnaChipIntegrator-v0.5.0-alpha.2

This is a pre-release (alpha) version.

Changes compared with version v0.5.0-alpha.1:

• Executable now installs as RnaChipIntegrator (i.e. no .py extension)
• Specify feature type (e.g. 'gene', 'transcript' etc) to be used in output using --feature option.
• New direction field in output indicates whether hits are up- or downstream from reference.
• Specify arbitrary columns from input peaks file using new --peak_cols options to set chromosome, start and end.
• --pad option is automatically implied by the --compact option (i.e. single line output is always padded).

RnaChipIntegrator-v0.5.0-alpha.1

Complete reimplementation of RnaChipIntegrator to unify internal algorithms, simplify usage and substantially update the documentation.

• No distinction is now made between 'summits' and 'peaks'; the same algorithm is applied in each case.
• The program always finds the nearest features 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 features are calculated from the TSS of the feature to whichever of the peak edges are closer; alternatively distances can be calculated between the nearest pair of peak/feature edges by specifying the --edge=both option.
• Any differential expression flags in the input features file are ignored unless the --only-DE option is specified, in which case only the differentially expressed features are considered in the analyses.
• By default each peak/feature pair is reported on a separate line; the --compact option reports all nearest features/peaks on a single line of output.
• Excel output is only produced if the --xls option is specified; summary output is only produced if --summary is specified.
• The rearrange_columns.py utility has been dropped.

RnaChipIntegrator-0.4.4

Patch/bug fix release:

• Use /usr/bin/env rather than /bin/env to invoke Python interpreter in RnaChipIntegrator.py. The use of `/bin/env' is broken for some Linux distributions (e.g. Ubuntu).

RnaChipIntegrator-0.4.3

• Adds a new output option --pad: for NearestTranscriptsToPeakEdge and NearestTSSToPeakEdge analyses, where necessary adds "blank" lines (i.e. only containing chromosome, start and end) to output files and spreadsheet so that each reported peak has the same number of lines associated regardless of the number of hits.
• Truncate worksheet titles if they exceed maximum length as defined by the spreadsheet writing libraries.