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lfproQC  

Quality Control for Label-Free Proteomics Expression Data
View on CRAN: Click here


Download and install lfproQC package within the R console
Install from CRAN:
install.packages("lfproQC")

Install from Github:
library("remotes")
install_github("cran/lfproQC")

Install by package version:
library("remotes")
install_version("lfproQC", "1.4.0")



Attach the package and use:
library("lfproQC")
Maintained by
Kabilan S
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2024-05-23
Latest Update: 2024-05-23
Description:
Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expressionanalysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluation measures were chosen for this study based on the research papers published by Välikangas et al. (2016) <doi:10.1093/bib/bbw095>, Jin et al. (2021) <doi:10.1038/s41598-021-81279-4> and Srivastava et al. (2023) <doi:10.2174/1574893618666230223150253>.
How to cite:
Kabilan S (2024). lfproQC: Quality Control for Label-Free Proteomics Expression Data. R package version 1.4.0, https://cran.r-project.org/web/packages/lfproQC. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.0 (2024-05-23 18:10), 0.2.0 (2024-09-06 15:00), 0.3.0 (2024-09-13 11:50), 1.3.0 (2024-09-30 09:20)
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Complete documentation for lfproQC
Functions, R codes and Examples using the lfproQC R package
Full lfproQC package functions and examples
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