v0.0.10

What's Changed

• updated Github actions
• updated command line interface
• removed unnecessary required field from create_pairing_from_file function

Full Changelog: v0.0.9...v0.0.10

v0.0.9

What's Changed

This is a major release.

• Added protein-group level FDR
• Added additional documentation and a FAQ
• Improved error handling for input files

Full Changelog: v0.0.6...v0.0.9

v0.0.8

Fix email metadata in setup.cfg.

v0.0.7

Fix the publishing to PyPI

v0.0.6

What's Changed

This is a major release.

• Added support for the following database search engines: MSAmanda, MSFragger, MSGF+, and Comet
• Added support for mzTab and pepXML file format
• Added mix-max, which is a PSM-level FDR control procedure. Details can be found at Keich et al. Journal of Proteome Research. 2015. https://pubs.acs.org/doi/10.1021/acs.jproteome.5b00081
• Added three peptide-level FDR control procedures: psm-only, peptide-only, and psm-peptide. Details can be found at Lin et al. Journal of Proteome Research. https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.2c00282
• Added two protein-level FDR control procedures: max and sum.

Full Changelog: v0.0.5...v0.0.6

crema v0.0.5

This release is a major update:

• Refactor of all classes/functions for better organization and readability
• Updated and improved unit/system tests
• Huge speed increase in calculating confidence level estimates

crema v0.0.4

This release is a minor update.

The vignette tab in crema's readthedocs page is now populated with its first tutorial on how to use crema at a basic level as a Python package.

crema v0.0.3

This release is a minor update.

• Grammar edits to the "Getting Started" page of crema's readthedocs page
• Uploaded a .svg file of the crema logo (to fix the broken image link on PyPI) and updated the README file to reflect this change
• In the results class, changed the "write_csv()" function to "write_file()" with optional parameter inputs of "output_dir" and "file_root" to allow the user to more easily specify the directory to write the results file to. Now writes files with the suffix "crema.psm_results.txt", as the CLI would.

crema v0.0.2

This release is a bug fix.

Bug: Reading in a tab delimited file (such as a .txt file) caused crema to throw the following error: "ValueError: Usecols do not match columns". Upon further investigation, discovered that the read file method could not properly identify column names even after specifying the separator equal to "\t".

Fix: When using the pandas read_csv method, specified the "sep" argument equal to "None", which uses Python's builtin sniffer tool to automatically detect the separator used in the input file.

crema v0.0.1

This is the first release of crema!

crema is a Python Package designed for Confidence Estimation for Mass Spectrometry Proteomics. Upon this first release, crema comes with both an API and a CLI. It can perform basic q-value calculations via target-decoy competition on files containing a collection of Peptide-Spectrum Matches.

Check out crema's documentation here:
https://crema-ms.readthedocs.io/

More confidence estimation methods will be implemented in the near future!