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dwctaxon, an R package for editing and validatingtaxonomic data in Darwin Core format dwctaxon 是一个 R 软件包，用于编辑和验证达尔文核心格式的分类数据
Journal of open source software Pub Date : 2024-01-12 DOI: 10.21105/joss.06215
Joel H. Nitta, W. Iwasaki
{"title":"dwctaxon, an R package for editing and validating\u0000taxonomic data in Darwin Core format","authors":"Joel H. Nitta, W. Iwasaki","doi":"10.21105/joss.06215","DOIUrl":"https://doi.org/10.21105/joss.06215","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"24 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139532729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
surtvep: An R package for estimating time-varying effects. 一个R包，用于估计时变效应。
Journal of open source software Pub Date : 2024-01-01 Epub Date: 2024-06-28 DOI: 10.21105/joss.05688
Lingfeng Luo, Wenbo Wu, Jeremy M G Taylor, Jian Kang, Michael J Kleinsasser, Kevin He
{"title":"surtvep: An R package for estimating time-varying effects.","authors":"Lingfeng Luo, Wenbo Wu, Jeremy M G Taylor, Jian Kang, Michael J Kleinsasser, Kevin He","doi":"10.21105/joss.05688","DOIUrl":"10.21105/joss.05688","url":null,"abstract":"<p><p>The surtvep package is an open-source software designed for estimating time-varying effects in survival analysis using the Cox non-proportional hazards model in R. With the rapid increase in large-scale time-to-event data from national disease registries, detecting and accounting for time-varying effects in medical studies have become crucial. Current software solutions often face computational issues such as memory limitations when handling large datasets. Furthermore, modeling time-varying effects for time-to-event data can be challenging due to small at-risk sets and numerical instability near the end of the follow-up period. surtvep addresses these challenges by implementing a computationally efficient Kronecker product-based proximal algorithm, supporting both unstratified and stratified models. The package also incorporates P-spline and smoothing spline penalties to improve estimation (Eilers & Marx, 1996). Cross-validation and information criteria are available to determine the optimal tuning parameters. Parallel computation is enabled to further enhance computational efficiency. A variety of operating characteristics are provided, including estimated time-varying effects, confidence intervals, hypothesis testing, and estimated hazard functions and survival probabilities. The surtvep package thus offers a comprehensive and flexible solution to analyzing large-scale time-to-event data with dynamic effect trajectories.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 98","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data. SCIMAP：用于多路复用成像数据综合空间分析的 Python 工具包。
Journal of open source software Pub Date : 2024-01-01 Epub Date: 2024-05-29 DOI: 10.21105/joss.06604
Ajit J Nirmal, Peter K Sorger
{"title":"SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data.","authors":"Ajit J Nirmal, Peter K Sorger","doi":"10.21105/joss.06604","DOIUrl":"10.21105/joss.06604","url":null,"abstract":"<p><p>Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors (\"Catching up with Multiplexed Tissue Imaging,\" 2022). A critical aspect of such \"tissue profiling\" is quantifying the spatial relationships among cells at different scales from the interaction of neighboring cells to recurrent communities of cells of multiple types. This often involves statistical analysis of 10<sup>7</sup> or more cells in which up to 100 biomolecules (commonly proteins) have been measured. While software tools currently cater to the analysis of spatial transcriptomics data (Liu et al., 2022), there remains a need for toolkits explicitly tailored to the complexities of multiplexed imaging data including the need to seamlessly integrate image visualization with data analysis and exploration. We introduce SCIMAP, a Python package specifically crafted to address these challenges. With SCIMAP, users can efficiently preprocess, analyze, and visualize large datasets, facilitating the exploration of spatial relationships and their statistical significance. SCIMAP's modular design enables the integration of new algorithms, enhancing its capabilities for spatial analysis.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 97","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11173324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PET2BIDS: a library for converting Positron Emission Tomography data to BIDS. PET2BIDS：将正电子发射断层扫描数据转换为 BIDS 的库。
Journal of open source software Pub Date : 2024-01-01 Epub Date: 2024-08-23 DOI: 10.21105/joss.06067
Anthony Galassi, Martin Norgaard, Adam G Thomas, Gabriel Gonzalez-Escamilla, Claus Svarer, Chris Rorden, Granville J Matheson, Gitte M Knudsen, Robert B Innis, Melanie Ganz, Cyrus Eierud, Murat Bilgel, Cyril Pernet
{"title":"PET2BIDS: a library for converting Positron Emission Tomography data to BIDS.","authors":"Anthony Galassi, Martin Norgaard, Adam G Thomas, Gabriel Gonzalez-Escamilla, Claus Svarer, Chris Rorden, Granville J Matheson, Gitte M Knudsen, Robert B Innis, Melanie Ganz, Cyrus Eierud, Murat Bilgel, Cyril Pernet","doi":"10.21105/joss.06067","DOIUrl":"10.21105/joss.06067","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 100","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11414599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142304913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
NEMSEER: A Python package for downloading and handlinghistorical National Electricity Market forecast data produced by theAustralian Energy Market Operator NEMSEER：用于下载和处理澳大利亚能源市场运营商制作的国家电力市场预测历史数据的 Python 软件包
Journal of open source software Pub Date : 2023-12-09 DOI: 10.21105/joss.05883
A. Prakash, A. Bruce, I. MacGill
{"title":"NEMSEER: A Python package for downloading and handling\u0000historical National Electricity Market forecast data produced by the\u0000Australian Energy Market Operator","authors":"A. Prakash, A. Bruce, I. MacGill","doi":"10.21105/joss.05883","DOIUrl":"https://doi.org/10.21105/joss.05883","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"11 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138585852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
spiketools: a Python package for analyzing single-unit neural activity spiketools:用于分析单个神经活动的Python包
Journal of open source software Pub Date : 2023-11-14 DOI: 10.21105/joss.05268
Thomas Donoghue, Sandra Maesta-Pereira, Claire Zhixian Han, Salman Ehtesham Qasim, Joshua Jacobs
{"title":"spiketools: a Python package for analyzing single-unit neural activity","authors":"Thomas Donoghue, Sandra Maesta-Pereira, Claire Zhixian Han, Salman Ehtesham Qasim, Joshua Jacobs","doi":"10.21105/joss.05268","DOIUrl":"https://doi.org/10.21105/joss.05268","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"18 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ER-Evaluation: End-to-End Evaluation of Entity Resolution Systems er评估:实体解决系统的端到端评估
Journal of open source software Pub Date : 2023-11-11 DOI: 10.21105/joss.05619
Olivier Binette, Jerome P. Reiter
{"title":"ER-Evaluation: End-to-End Evaluation of Entity Resolution Systems","authors":"Olivier Binette, Jerome P. Reiter","doi":"10.21105/joss.05619","DOIUrl":"https://doi.org/10.21105/joss.05619","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"53 23","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135041597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MAHOS: Measurement Automation Handling and Orchestration System MAHOS:测量自动化处理和编排系统
Journal of open source software Pub Date : 2023-11-11 DOI: 10.21105/joss.05938
Kosuke Tahara
{"title":"MAHOS: Measurement Automation Handling and Orchestration System","authors":"Kosuke Tahara","doi":"10.21105/joss.05938","DOIUrl":"https://doi.org/10.21105/joss.05938","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"54 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135041592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using the tidyverse with terra objects: the tidyterra package 使用tidyverse和terra对象:tidyterra包
Journal of open source software Pub Date : 2023-11-10 DOI: 10.21105/joss.05751
Diego Hernangómez
{"title":"Using the tidyverse with terra objects: the tidyterra package","authors":"Diego Hernangómez","doi":"10.21105/joss.05751","DOIUrl":"https://doi.org/10.21105/joss.05751","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"123 10","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135136743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique OpenFEPOPS: FEPOPS分子相似性技术的Python实现
Journal of open source software Pub Date : 2023-11-09 DOI: 10.21105/joss.05763
Yan-Kai Chen, Douglas R. Houston, Manfred Auer, Steven Shave
{"title":"OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique","authors":"Yan-Kai Chen, Douglas R. Houston, Manfred Auer, Steven Shave","doi":"10.21105/joss.05763","DOIUrl":"https://doi.org/10.21105/joss.05763","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":" 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135241389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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