rnachipintegrator - 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).

- Python
Published by pjbriggs about 2 years ago

rnachipintegrator - RnaChipIntegrator-v2.0.0

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

- Python
Published by pjbriggs about 6 years ago

rnachipintegrator - 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).

- Python
Published by pjbriggs over 6 years ago

rnachipintegrator - 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 https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/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 https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/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 https://github.com/fls-bioinformatics-core/RnaChipIntegrator/pull/46)

- Python
Published by pjbriggs over 7 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs about 8 years ago

rnachipintegrator - RnaChipIntegrator-v1.0.2

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

- Python
Published by pjbriggs over 9 years ago

rnachipintegrator - RnaChipIntegrator-v1.0.1

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

- Python
Published by pjbriggs almost 10 years ago

rnachipintegrator - 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/

- Python
Published by pjbriggs about 10 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs about 10 years ago

rnachipintegrator - 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).

- Python
Published by pjbriggs about 10 years ago

rnachipintegrator - 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)

- Python
Published by pjbriggs about 10 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs about 10 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs over 10 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs over 10 years ago

rnachipintegrator - 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).

- Python
Published by pjbriggs over 10 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs over 10 years ago

rnachipintegrator - 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).

- Python
Published by pjbriggs almost 11 years ago

rnachipintegrator - 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.

- Python
Published by pjbriggs over 11 years ago