crisprzip - 1.2.2

[1.2.2] - 2025-07-31

Fixed

• Proper loading of parameter set 'sequence_params', including NA weight.

- Python
Published by hiddeoff 7 months ago

crisprzip - 1.2.1 [YANKED]

[1.2.1] - 2025-07-31 [YANKED]

Fixed

• Sequence and average parameter sets are updated to correspond with the proper R-loop cost calculations.

Added

• Functionality to save R-loop cost weighing as parameter 'weight' to parameter sets and load them as a BareSearcher attribute.
• Function to load binding rates from parameter set files.

- Python
Published by hiddeoff 7 months ago

crisprzip -

[1.2.0] - 2025-07-08

Fixed

• Major bugfix: R-loop cost is now properly converted to units kBT (at room temperature, 20 Celsius). In all previous versions, R-loop cost was reported in units kcal/mol, being a factor ~1.7 too small.
• End-to-end test no longer passes automatically. Test values are updated according to new R-loop costs.

Added

• Inclusion of Nearest-Neighbor values from Banerjee et al. (2020) for RNA/DNA hybrids at physiological salt conditions (100 mM NaCl). Support for these values is quite limited; they are only available for matching hybrid basepairs, and no similar salt correction can yet be made for the dsDNA base pairs.
• A set of sequence parameters for a smooth protein landscape. However, these values will be replaced soon (see Notes below).

Notes

• With the R-loop cost being corrected, new sequence-dependent energy landscapes should be generated and included with this package. This makes version 1.2.0 a temporary version, and the more stable 1.2.1 will follow very soon.

- Python
Published by hiddeoff 8 months ago

crisprzip - 1.1.1

[1.1.1] - 2025-04-08

Bugfix

• More robust approach to checking sequence input. Any sequence (protospacer/off-target) can now be offered in a 20/23/24 nt format.

- Python
Published by hiddeoff 11 months ago

crisprzip - 1.1.0

[1.1.0] - 2024-02-18

Added

• Function load_landscape in crisprzip.kinetics for robust parameter loading
• Cross-platform testing: MacOS, Ubuntu, Windows for Python 3.10, 3.11, 3.12

Bugfix

• Parameters for nucleic acid stability and landscape definitions are now included as package data which avoids relative path issues.

- Python
Published by hiddeoff about 1 year ago

crisprzip - First release of CRISPRzip

This version marks the first stable release of CRISPRzip. Feedback and contributions are welcome to improve the project.

- Python
Published by hiddeoff about 1 year ago