Seismic-rna

New Features

- New command `seismic pool` allows you to pool samples after `seismic relate`. The archetypal use case would be if you have two or more replicate samples and you want to pool them to treat them as one sample.

Documentation

- Documentation has been updated to include `seismic pool`.

API Internals

- `seismicrna.core.data` has been largely rewritten to accommodate pooled datasets.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.10.0...v0.11.0

Features

- Five new types of graphs:

- `histpos`: histogram of mutations per position
- `histread`: histogram of mutations per read
- `roc`: receiver operating characteristic (ROC)
- `aucroll`: rolling area under the curve of ROC
- `corroll`: rolling correlation/comparison between profiles

- Graphs `seqbar` and `diffbar` were renamed to `profile` and `delprof`, respectively.
- Graphs that compare pairs of tables (`corroll`, `delprof`, and `scatter`) can now compare all combinations of 2 tables from a list (with `--comppair`) as well as compare each table to itself (with `--compself`).

Documentation

- Documentation for how to use the main workflow is now up to date.

What's Changed
* 0.10.0 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/9


**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.8...v0.10.0

Bugfixes

- Fixed bug where VARNA color values would be output in scientific notation instead of plain decimal notation, causing some programs to fail when parsing them.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.7...v0.9.8

Bug fixes

- Patched bug where `--include-gu` would make SEISMIC-RNA crash. Credit to justinaruda.

Documentation

- Add Justin Aruda (justinaruda) to list of authors.

What's Changed
* 0.9.6 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/8


**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.6...v0.9.7

Features
- New option `--all-pos/unmasked-pos` in `seismic export web` enables toggling between exporting only unmasked positions (default, and the only option in v0.9.5) and all positions.

**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.5...v0.9.6

Performance
- The function `apply_mask` has been made more efficient in the common case that most of the reads are kept. Credit to justinaruda.

Documentation
- Documentation for the main workflow has been updated.

What's Changed
* Optimized masking by replacing np.intersect1d() with np.setdiff1d(). by justinaruda in https://github.com/rouskinlab/seismic-rna/pull/5
* Improved np.setdiff1d() logic during masking. by justinaruda in https://github.com/rouskinlab/seismic-rna/pull/6
* 0.9.5 by matthewfallan in https://github.com/rouskinlab/seismic-rna/pull/7


**Full Changelog**: https://github.com/rouskinlab/seismic-rna/compare/v0.9.4...v0.9.5