Merge pull request #48 from SwiftSeal/citation

Citation

Author: SwiftSeal

CITATION.bib

@@ -1,11 +1,13 @@
-@article {Smith2024.02.14.580321,
-	author = {Smith, Moray and Jones, John T. and Hein, Ingo},
-	title = {Resistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation},
-	elocation-id = {2024.02.14.580321},
-	year = {2024},
-	doi = {10.1101/2024.02.14.580321},
-	publisher = {Cold Spring Harbor Laboratory},
-	URL = {https://www.biorxiv.org/content/early/2024/04/03/2024.02.14.580321},
-	eprint = {https://www.biorxiv.org/content/early/2024/04/03/2024.02.14.580321.full.pdf},
-	journal = {bioRxiv}
+@article{doi:10.1177/11779322241308944,
+	author = {Moray Smith and John T Jones and Ingo Hein},
+	title ={Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae},
+	journal = {Bioinformatics and Biology Insights},
+	volume = {19},
+	number = {},
+	pages = {11779322241308944},
+	year = {2025},
+	doi = {10.1177/11779322241308944},
+	URL = {https://doi.org/10.1177/11779322241308944},
+	eprint = {https://doi.org/10.1177/11779322241308944},
+	abstract = {Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements.}
 }

README.md

@@ -7,6 +7,8 @@
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/swiftseal/resistify/blob/main/assets/resistify.ipynb)
 [![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh)
 
+[*Resistify is now published!*](https://doi.org/10.1177/11779322241308944)
+
 </div>
 
 Resistify is a program which rapidly identifies and classifies plant resistance genes from protein sequences.
@@ -31,12 +33,12 @@ When using `conda`, please ensure that your Bioconda has been [configured correc
 Docker/Podman containers are also available through the [biocontainers repository](https://quay.io/repository/biocontainers/resistify?tab=tags).
 To use these with - for example - `singularity`, simply run:
 
-`singularity exec docker://quay.io/biocontainers/resistify:<tag-goes-here>`
+`singularity exec docker://quay.io/biocontainers/resistify:<tag-goes-here> resistify`
 
 If you are having issues with `conda`, you can instead try installing directly from the repository:
 
 ```sh
-pip install https://github.com/SwiftSeal/resistify/archive/refs/tags/v1.1.3.tar.gz
+pip install https://github.com/SwiftSeal/resistify/archive/refs/tags/v1.1.4.tar.gz
 ```
 
 Note that `resistify` requires `hmmer` to be installed and available in your system's PATH, which will not be installed automatically when using `pip`.
@@ -311,7 +313,7 @@ If you have any suggestions for additional features, get in touch!
 
 ## Citing
 
-> Smith, M., Jones, J. T., & Hein, I. (2024). Resistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation. *bioRxiv*, 2024-02. https://doi.org/10.1101/2024.02.14.580321
+> Smith M., Jones J. T., Hein I. (2025) Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae. *Bioinformatics and Biology Insights*. 2025;19. [doi:10.1177/11779322241308944](https://doi.org/10.1177/11779322241308944)
 
 You must also cite:
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "resistify"
-version = "1.1.3"
+version = "1.1.4"
 dependencies = [
   "scikit-learn>=0.24.2",
   "numpy",

resistify/__version__.py

@@ -1 +1 @@
-__version__ = "1.1.3"
+__version__ = "1.1.4"

resistify/main.py

@@ -246,7 +246,7 @@ def main():
 
     logger.info("Thank you for using Resistify!")
     logger.info("If you used Resistify in your research, please cite the following:")
-    logger.info(" - Resistify: https://doi.org/10.1101/2024.02.14.580321")
+    logger.info(" - Resistify: https://doi.org/10.1177/11779322241308944")
     logger.info(" - NLRexpress: https://doi.org/10.3389/fpls.2022.975888")
     if args.command == "prr":
         logger.info(" - TMbed: https://doi.org/10.1186/s12859-022-04873-x")