ClinicalTranscriptLink is a package that aims to identify correlations
between clinical expression of cancers and the transcriptional
expression of genes using bulk RNA sequencing data. Packages currently
available only study one of these and do not provide much correlation
between the clinical expression of diseases and the corresponding gene
expression. As such, this package aims to create that link to help us
better understand the relation. Specifically, the package aims to
study: - 1) the type of cancer and its relation to gene expression - 2)
the survival analysis of different types of cancer
This package contains functions to perform analysis as well as
visualisation of the above two goals. The ClinicalTranscriptLink
package was developed using R version 4.3.1 (2023-06-16),
Platform: x86_64-w64-mingw32/x64 (64-bit) and
Running under: Windows 11 x64 (build 22631).
You can install the development version of ClinicalTranscriptLink from GitHub with:
# install.packages("devtools")
devtools::install_github("michellemlin/ClinicalTranscriptLink", build_vignettes = TRUE)
library(ClinicalTranscriptLink)To run the Shiny app:
ClinicalTranscriptLink::runClinicalTranscriptLink()For an example of use of ClinicalTranscriptLink:
ls("package:ClinicalTranscriptLink")
data(package = "ClinicalTranscriptLink")
browseVignettes("ClinicalTranscriptLink")ClinicalTranscriptLink provides the following functions at the moment:
-
metadataExtract: a function that allows users to extract metadata from from clinical data -
mergeClinicalRNA: a function that allows users to merge the clinical dataset with the RNASeq dataset -
survivalAnalyse: a function that allows for analysis of survival rates -
heatmapGenerate: a function to create a heatmap of gene expression based on clinical features -
integrityCheckClinical: a function to check integrity of datasets -
runClinicalTranscriptLink: a function to run the Shiny App
This package was created by Michelle Lin and contains functions found
in packages survival, survminer, dplyr for survival analysis and
DESeq2 that will be used for differential expression analysis.
ClinicalTranscriptLink provides the following functions at the moment
and contributions are:
-
metadataExtract: The author wrote this function using base R functions. Open AI was used to search for potential functions but structure and logic was by author -
mergeClinicalRNA: The author wrote this function using baseR functions. Open AI was used to search for potential functions and debugging but logic was by author. -
survivalAnalyse: This function was written by author and utilise functions in thesurvivallibrary. -
heatmapGenerate: The author wrote this function and made design decisions. Open AI was used to search for potential functions and debugging purposes. -
integrityCheckClinical: This function was written by author with the help of OpenAI for function search -
runClinicalTranscriptLink: a function to run the Shiny App
All of the error checking and logic was done by author.
-
H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
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Kosinski M (2023). RTCGA.clinical: Clinical datasets from The Cancer Genome Atlas Project. doi:10.18129/B9.bioc.RTCGA.clinical https://doi.org/10.18129/B9.bioc.RTCGA.clinical, R package version 20151101.30.0, https://bioconductor.org/packages/RTCGA.clinical.
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Kosinski M (2023). RTCGA.rnaseq: Rna-seq datasets from The Cancer Genome Atlas Project. doi:10.18129/B9.bioc.RTCGA.rnaseq https://doi.org/10.18129/B9.bioc.RTCGA.rnaseq, R package version 20151101.30.0, https://bioconductor.org/packages/RTCGA.rnaseq.
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Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 (2014)
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R Core Team (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
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Therneau T (2023). A Package for Survival Analysis in R. R package version 3.5-5, https://CRAN.R-project.org/package=survival.
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Kassambara A, Kosinski M, Biecek P (2021). survminer: Drawing Survival Curves using ‘ggplot2’. R package version 0.4.9, https://CRAN.R-project.org/package=survminer.
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Wickham H, Francois R, Henry L, Muller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.
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OpenAI. (2023). GPT-3.5: A language model by OpenAI. https://www.openai.com/gpt-3.5
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Testing Package (2023). Anjali Silva
This package was developed as part of an assessment for Fall 2023 BCB410H1: Applied Bioinformatics course at the University of Toronto, Toronto, CANADA. ClinicalTranscriptLink welcomes issues, enhancement requests, and other contributions. To submit an issue, use the GitHub issues.
The package may take a while to build as the vignettes have datasets that are really large and thus, take a long time to build.