Initial commit

Author: aedin

.DS_Store

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+# Auto detect text files and perform LF normalization
+* text=auto

.gitattributes

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/

.gitignore

@@ -0,0 +1,14 @@
+{
+  "hash": "2ff41a1a54248d30d70150344493982a",
+  "result": {
+    "markdown": "---\ntitle: Lauren L Hsu\nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com \n    - icon: house-door\n      text: Homepage\n      href: https://www.homepage.com \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\n\ndescription: \n  Gradudate Student\nimage: ../../contents/photos/people/laurenhsu.png\ncard_style: \"summary_large_image\"\ncategories:\n  - Graduate Student\n  - Spatial Biology\n  - Human Cell Atlas\n---\n\n\n## Lauren L. Hsu\n\n## Links\n\n[ORCID](https://orcid.org/..)\n\n# Publications\n\nFull list of publications see [Google Scholar](https://scholar.google.com/..)\n\nRecent publications include\n\n\n::: {.cell}\n::: {.cell-output .cell-output-stdout}\n```\n[1] S. Y. Chin, Y. C. Poh, A. Kohler, et al. \"Additive manufacturing of\nhydrogel-based materials for next-generation implantable medical\ndevices\". Eng. In: _Science robotics_ 2.2 (Jan. 2017). ISSN: 2470-9476.\nDOI: 10.1126/scirobotics.aah6451. PMID: 31289767.\n\n[2] L. L. Hsu and A. C. Culhane. \"Correspondence analysis for dimension\nreduction, batch integration, and visualization of single-cell RNA-seq\ndata\". Eng. In: _Scientific reports_ 13.1 (Jan. 2023), p. 1197. ISSN:\n2045-2322. DOI: 10.1038/s41598-022-26434-1. PMID: 36681709.\n\n[3] L. L. Hsu and A. C. Culhane. \"Impact of Data Preprocessing on\nIntegrative Matrix Factorization of Single Cell Data\". Eng. In:\n_Frontiers in oncology_ 10 (Jun. 2020), p. 973. ISSN: 2234-943X. DOI:\n10.3389/fonc.2020.00973. PMID: 32656082.\n```\n:::\n:::\n",
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.quarto/_freeze/Alumni/LaurenHsu/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "5cd919adce5bfd91fb21a7d33f6eb5d1",
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+    "markdown": "---\ntitle: Dr. Eanna Fennell\nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com \n    - icon: house-door\n      text: Homepage\n      href: https://www.homepage.com \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\n\ndescription: \n  Postdoctoral fellow in the Murray Lab\nimage: ../../contents/photos/people/eannafennell.png\ncard_style: \"summary_large_image\"\ncategories:\n  - Postdoctoral fellow\n  - Spatial Biology\n  - Human Cell Atlas\n---\n\n\n## Dr. Eanna Fennell\n\n## Links\n\n[ORCID](https://orcid.org/..)\n\n# Publications\n\nFull list of publications see [Google Scholar](https://scholar.google.com/..)\n\nRecent publications include\n\n\n::: {.cell}\n::: {.cell-output .cell-output-stdout}\n```\n[1] F. Berditchevski, E. Fennell, and P. G. Murray. \"Calcium-dependent\nsignalling in B-cell lymphomas\". Eng. In: _Oncogene_ 40.45 (Nov. 2021),\npp. 6321-6328. ISSN: 1476-5594. DOI: 10.1038/s41388-021-02025-8. PMID:\n34625709.\n\n[2] E. Fennell and J. M. Huyghe. \"Chemically Responsive Hydrogel\nDeformation Mechanics: A Review\". Eng. In: _Molecules (Basel,\nSwitzerland)_ 24.19 (Sep. 2019). ISSN: 1420-3049. DOI:\n10.3390/molecules24193521. PMID: 31569433.\n\n[3] E. Fennell, J. Kamphus, and J. M. Huyghe. \"The Importance of the\nMixing Energy in Ionized Superabsorbent Polymer Swelling Models\". Eng.\nIn: _Polymers_ 12.3 (Mar. 2020). ISSN: 2073-4360. DOI:\n10.3390/polym12030609. PMID: 32155977.\n\n[4] M. Nohtani, K. Vrzalikova, M. Ibrahim, et al. \"Impact of Tumour\nEpstein-Barr Virus Status on Clinical Outcome in Patients with\nClassical Hodgkin Lymphoma (cHL): A Review of the Literature and\nAnalysis of a Clinical Trial Cohort of Children with cHL\". Eng. In:\n_Cancers_ 14.17 (Sep. 2022). ISSN: 2072-6694. DOI:\n10.3390/cancers14174297. PMID: 36077832.\n\n[5] K. I. Notarte, S. Senanayake, I. Macaranas, et al. \"MicroRNA and\nOther Non-Coding RNAs in Epstein-Barr Virus-Associated Cancers\". Eng.\nIn: _Cancers_ 13.15 (Aug. 2021). ISSN: 2072-6694. DOI:\n10.3390/cancers13153909. PMID: 34359809.\n\n[6] H. Pearce, W. Croft, S. M. Nicol, et al. \"Tissue-resident memory T\ncells in pancreatic ductal adenocarcinoma co-express PD-1 and TIGIT and\nfunctional inhibition is reversible by dual antibody blockade\". Eng.\nIn: _Cancer immunology research_ (Jan. 2023). ISSN: 2326-6074. DOI:\n10.1158/2326-6066.CIR-22-0121. PMID: 36689623.\n\n[7] E. Syrimi, E. Fennell, A. Richter, et al. \"The immune landscape of\nSARS-CoV-2-associated Multisystem Inflammatory Syndrome in Children\n(MIS-C) from acute disease to recovery\". Eng. In: _iScience_ 24.11\n(Nov. 2021), p. 103215. ISSN: 2589-0042. DOI:\n10.1016/j.isci.2021.103215. PMID: 34632327.\n```\n:::\n:::\n",
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.quarto/_freeze/Partners/EannaFennell/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "2ff41a1a54248d30d70150344493982a",
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+    "markdown": "---\ntitle: Lauren L Hsu\nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com \n    - icon: house-door\n      text: Homepage\n      href: https://www.homepage.com \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\n\ndescription: \n  Gradudate Student\nimage: ../../contents/photos/people/laurenhsu.png\ncard_style: \"summary_large_image\"\ncategories:\n  - Graduate Student\n  - Spatial Biology\n  - Human Cell Atlas\n---\n\n\n## Lauren L. Hsu\n\n## Links\n\n[ORCID](https://orcid.org/..)\n\n# Publications\n\nFull list of publications see [Google Scholar](https://scholar.google.com/..)\n\nRecent publications include\n\n\n::: {.cell}\n::: {.cell-output .cell-output-stdout}\n```\n[1] S. Y. Chin, Y. C. Poh, A. Kohler, et al. \"Additive manufacturing of\nhydrogel-based materials for next-generation implantable medical\ndevices\". Eng. In: _Science robotics_ 2.2 (Jan. 2017). ISSN: 2470-9476.\nDOI: 10.1126/scirobotics.aah6451. PMID: 31289767.\n\n[2] L. L. Hsu and A. C. Culhane. \"Correspondence analysis for dimension\nreduction, batch integration, and visualization of single-cell RNA-seq\ndata\". Eng. In: _Scientific reports_ 13.1 (Jan. 2023), p. 1197. ISSN:\n2045-2322. DOI: 10.1038/s41598-022-26434-1. PMID: 36681709.\n\n[3] L. L. Hsu and A. C. Culhane. \"Impact of Data Preprocessing on\nIntegrative Matrix Factorization of Single Cell Data\". Eng. In:\n_Frontiers in oncology_ 10 (Jun. 2020), p. 973. ISSN: 2234-943X. DOI:\n10.3389/fonc.2020.00973. PMID: 32656082.\n```\n:::\n:::\n",
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.quarto/_freeze/Partners/LaurenHsu/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "edcf132be1cccf0e188489b51aa2b572",
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+    "markdown": "---\ntitle: Dr Olywn Mahon \nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com \n    - icon: house-door\n      text: Homepage\n      href: https://www.homepage.com \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\n\ndescription: \n  Post doctoral fellow in \nimage: ../../contents/photos/people/olywnmahon .png\ncard_style: \"summary_large_image\"\ncategories:\n  - Postdoctorial Fellow\n  - scRNAseq\n---\n\n\n## Dr. Olywn Mahon\n\n## Links\n\n[ORCID](https://orcid.org/..)\n\n# Publications\n\nFull list of publications see [Google Scholar](https://scholar.google.com/..)\n\nRecent publications include\n\n\n::: {.cell}\n::: {.cell-output .cell-output-stderr}\n```\nNo Results.\n```\n:::\n\n::: {.cell-output .cell-output-stdout}\n```\nNULL\n```\n:::\n:::\n",
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.quarto/_freeze/Partners/OlywnMahon/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "cf3f1111b745362b517dbf7e19d2acb8",
+  "result": {
+    "markdown": "---\ntitle: Prof Aedin Culhane\nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com/in/aedinculhane/  \n    - icon: house-door\n      text: Homepage\n      href: https://www.linkedin.com/in/aedinculhane/  \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\ndescription: \n  Professor, University of Limerick\nimage: ../../contents/photos/people/aedinculhane.png\ncard_style: \"summary_large_image\"\ncategories:\n  - PI\n  - Group Leader\n  - LDCRC\n---\n\n\n## Prof Aedin Culhane\n\nAedín Culhane is a Professor of Biomedical Sciences (Cancer Genomics) in the UL School of Medicine. She is a computational oncologist with expertise in multi-omics data integration, statistical genomics, clinical bioinformatics and genomics in oncology. She has over 20 years' experience in cancer genomics, of which over 15 years were in the [Dana-Farber Cancer Institute](https://www.dana-farber.org/research/departments-centers-and-labs/departments-and-centers/department-of-data-science/) and [Harvard TH Chan School of Public Health in Boston, USA](https://www.hsph.harvard.edu/biostatistics/). Her recent research focuses on algorithm development and integrative data of single cell molecular data in cancer to identify molecules that regulate and can be targeted during tumour development, progression, drug response and resistance. She is a member of the Human Cell Atlas (https://www.humancellatlas.org ) project. She is a leader in the Bioconductor ([www.bioconductor.org](http://www.bioconductor.org/)) community, a global open source, open development software in R for genomics and an advocate for open source science.\n\n# Publications\n\n[Google Scholar](https://scholar.google.com/citations?user=O8OszPcAAAAJ)\n\n\n::: {.cell}\n\n:::\n",
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.quarto/_freeze/People/AedinCulhane/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "f7806ed1c6dc76b71631593ed5de51bb",
+  "result": {
+    "markdown": "---\ntitle: Mr Ahmad Alkhan \nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com/in/ahmad-alkhan-31311d/\n    - icon: house-door\n      text: Homepage\n      href: https://www.homepage.com \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\n\ndescription: \n  Graduate Student\nimage: ../../contents/photos/people/ahmadalkhan.jpeg\ncard_style: \"summary_large_image\"\ncategories:\n  - PhD Student\n  - Human Cell Atlas\n  - CZI\n---\n\n\n## Mr Ahmad Alkhan\n\n## Links\n\n[ORCID](https://orcid.org/..)\n\n# Publications\n\nFull list of publications see [Google Scholar](https://scholar.google.com/..)\n\nRecent publications include\n\n\n::: {.cell}\n::: {.cell-output .cell-output-stdout}\n```\n[1] M. F. Ahmad, A. Alim, N. S. Sen, et al. \"Electron microscopic\nstudies of the corpuscles of Stannius of an airbreathing teleost\n(Heteropneustes fossilis)\". Eng. In: _Journal of biosciences_ 27.5\n(Sep. 2002), pp. 509-13. ISSN: 0250-5991. DOI: 10.1007/BF02705048.\nPMID: 12381875.\n\n[2] W. Ahmad, S. Asaf, A. Khan, et al. \"Complete chloroplast genome\nsequencing and comparative analysis of threatened dragon trees Dracaena\nserrulata and Dracaena cinnabari\". Eng. In: _Scientific reports_ 12.1\n(Oct. 2022), p. 16787. ISSN: 2045-2322. DOI:\n10.1038/s41598-022-20304-6. PMID: 36202844.\n\n[3] S. Asaf, W. Ahmad, A. Al-Harrasi, et al. \"Uncovering the first\ncomplete plastome genomics, comparative analyses, and phylogenetic\ndispositions of endemic medicinal plant Ziziphus hajarensis\n(Rhamnaceae)\". Eng. In: _BMC genomics_ 23.1 (Jan. 2022), p. 83. ISSN:\n1471-2164. DOI: 10.1186/s12864-022-08320-2. PMID: 35086490.\n```\n:::\n:::\n",
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.quarto/_freeze/People/AhmadAlkhan/execute-results/html.json

@@ -0,0 +1,14 @@
+{
+  "hash": "31b978ecd4727a5db8cfcdbdd287751e",
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+    "markdown": "---\ntitle: Lauren L Hsu\nabout:\n  template: solana\n  image-width: 10em\n  image-shape: round\n  links:\n    - icon: twitter\n      text: twitter\n      href: https://twitter.com\n    - icon: github\n      text: Github\n      href: https://github.com\n    - icon: linkedin\n      text: LinkedIn\n      href: https://www.linkedin.com/in/lauren-hsu-155a282a/ \n    - icon: house-door\n      text: Homepage\n      href: https://www.homepage.com \n    - icon: envelope\n      text: email\n      href: mailto:[email protected]\n\ndescription: \n  Gradudate Student\nimage: ../../contents/photos/people/laurenhsu.jpeg\ncard_style: \"summary_large_image\"\ncategories:\n  - Graduate Student\n  - Spatial Biology\n  - Human Cell Atlas\n---\n\n\n## Lauren L. Hsu\n\n## Links\n\n[ORCID](https://orcid.org/..)\n\n# Publications\n\nFull list of publications see [Google Scholar](https://scholar.google.com/..)\n\nRecent publications include\n\n\n::: {.cell}\n::: {.cell-output .cell-output-stdout}\n```\n[1] S. Y. Chin, Y. C. Poh, A. Kohler, et al. \"Additive manufacturing of\nhydrogel-based materials for next-generation implantable medical\ndevices\". Eng. In: _Science robotics_ 2.2 (Jan. 2017). ISSN: 2470-9476.\nDOI: 10.1126/scirobotics.aah6451. PMID: 31289767.\n\n[2] L. L. Hsu and A. C. Culhane. \"Correspondence analysis for dimension\nreduction, batch integration, and visualization of single-cell RNA-seq\ndata\". Eng. In: _Scientific reports_ 13.1 (Jan. 2023), p. 1197. ISSN:\n2045-2322. DOI: 10.1038/s41598-022-26434-1. PMID: 36681709.\n\n[3] L. L. Hsu and A. C. Culhane. \"Impact of Data Preprocessing on\nIntegrative Matrix Factorization of Single Cell Data\". Eng. In:\n_Frontiers in oncology_ 10 (Jun. 2020), p. 973. ISSN: 2234-943X. DOI:\n10.3389/fonc.2020.00973. PMID: 32656082.\n```\n:::\n:::\n",
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