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#	README.md

README.md

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 # HTT: R data package
 
 Data, scripts, and functions of the High-Throughput
-Truthing project (HTT project). There are also functions
-and scripts replicating analyses done for different
-presentations and publications (in the "inst" directory).
+Truthing project (HTT project). The "inst" directory 
+will be used to archive scripts that reproduce the
+analyses done for different presentations and publications.
 
-Project hub space: https://ncihub.org/groups/eedapstudies
+To install this package from the R command line: install_github('DIDSR/HTT')
 
-Manuscript describing the project:
+#### Data and Code Repository
+* [https://github.com/DIDSR/HTT](https://github.com/DIDSR/HTT)
 
-* Dudgeon et al. (2020), "A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study," *Journal of Pathology Informatics*, **12**, p. 45. https://www.doi.org/10.4103/jpi.jpi_83_20
+#### Manual documenting the data and functions in the R package:
+* [https://github.com/DIDSR/HTT/tree/main/inst/manual](https://github.com/DIDSR/HTT/tree/main/inst/manual)
 
-Manuscript describing expert panel:
+#### Manuscript describing the project:
+* S. N. Dudgeon et al., “A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study,” arXiv:2010.06995, 2020. Accepted for publication by the Journal of Pathology Informatics, 2021. [https://arxiv.org/abs/2010.06995](https://arxiv.org/abs/2010.06995)
 
-* Garcia et al. (2022 - Submitted). "Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer," *Cancers*.
+#### Webinar tour of the data: [Video here](https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:TourofHTTData)
 
-Pathology Informatics Presentation:
-
-* B. D. Gallas and et al., “High Throughput Truthing (HTT): pathologist agreement from a pilot study,” presented at the Pathology Informatics Summit, 2021.  https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:PathologyInformaticsSummitHTTproject
+#### Version 1.0: Pathology Informatics Presentation:
+Version 1.0 of this repository holds the data, scripts, and functions that were used for the following presentation.
+* B. D. Gallas and et al., “High Throughput Truthing (HTT): pathologist agreement from a pilot study,” presented at the Pathology Informatics Summit, 2021.  [https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:PathologyInformaticsSummitHTTproject](https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:PathologyInformaticsSummitHTTproject)
 * R markdown to create the figures from this presentation
-can be found in this folder: inst/extra/20210505-PathologyInformatics
+can be found in this folder: [https://github.com/DIDSR/HTT/tree/main/inst/extra/20210505-PathologyInformatics](https://github.com/DIDSR/HTT/tree/main/inst/extra/20210505-PathologyInformatics)
+
+
+[comment]: <> "[![Github All Releases](https://img.shields.io/github/downloads/DIDSR/HTT/total)]()"
 
-[Link to project library](https://www.zotero.org/groups/4384613/eedap_studies_presentations_publications_and_studies/library/)