diff --git a/Changelog b/Changelog index e1d184f8..54b99c0d 100644 --- a/Changelog +++ b/Changelog @@ -1,7 +1,4 @@ -### Added - - -### Changed - - -### Fixed \ No newline at end of file +### Fixed +- Fixed the protein coverage calculations with partially overlapping and subsumed peptides +- Fixed an issue where peptides would map to multiple locations in the protein after having I/L converted (Needs to be used with MSFragger v3.6.1 or higher) +- Fixed an issue with report tables having no isobaric labels being reported \ No newline at end of file diff --git a/Makefile b/Makefile index 9e7ea8b5..c07ce4e3 100644 --- a/Makefile +++ b/Makefile @@ -6,8 +6,8 @@ BINARY = philosopher VERSION = $(shell date +%Y%m%d) BUILD = $(shell date +%Y%m%d%H%M) -TAG = v4.7.1 -RC = RC-2 +TAG = v4.8.0 +RC = RC LDFLAGS = -ldflags "-w -s -extldflags -static -X main.version=${TAG} -X main.build=${BUILD}" diff --git a/README.md b/README.md index 25590447..d037ec22 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,13 @@

[![Release](https://img.shields.io/github/release/nesvilab/philosopher.svg?color=purple&style=for-the-badge)](https://github.com/Nesvilab/philosopher/releases/latest) -![Golang](https://img.shields.io/badge/Go-1.19.3-blue.svg?style=for-the-badge) +![Golang](https://img.shields.io/badge/Go-1.19.4-blue.svg?style=for-the-badge) [![Go Report Card](https://goreportcard.com/badge/github.com/Nesvilab/philosopher?style=for-the-badge&color=red&logo=appveyor)](https://goreportcard.com/report/github.com/Nesvilab/philosopher) ![GitHub](https://img.shields.io/github/license/Nesvilab/philosopher?style=for-the-badge) ![](https://img.shields.io/github/downloads/Nesvilab/philosopher/total.svg?color=red&style=for-the-badge) ![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/Nesvilab/philosopher/go.yml?style=for-the-badge) -#### Philosopher is fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery. +#### Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery. - Database downloading and formatting. @@ -36,6 +36,7 @@ - Multi-level detailed reports for peptides, ions, and proteins. +- Support for REPRINT and MSstats. ## Download Download the latest version [here](https://github.com/nesvilab/philosopher/releases/latest). @@ -61,14 +62,11 @@ If you have any questions or remarks please use the [Discussion board](https://g ## How to cite da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI. [Philosopher: a versatile toolkit for shotgun proteomics data analysis](https://doi.org/10.1038/s41592-020-0912-y). Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848. -## About the developers -[Felipe da Veiga Leprevost](http://prvst.github.io) +## About the authors, and contributors +[Felipe da Veiga Leprevost (main author)](http://prvst.github.io) [Sarah Haynes](https://scholar.google.com/citations?user=HtRSUKkAAAAJ&hl=en) [Guo Ci Teo](https://github.com/guoci) [Alexey Nesvizhskii's research group](http://www.nesvilab.org/) - -## License -GPL 3