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MiRNAQCD

Micro-RNA Quality Control and Diagnosis

A complete and dedicated analytical toolbox for quality control and diagnosis based on subject-related measurements of micro-RNA (miRNA) expressions. The package consists of a set of functions that allow to train, optimize and use a Bayesian classifier that relies on multiplets of measured miRNA expressions. The package also implements the quality control tools required to preprocess input datasets. In addition, the package provides a function to carry out a statistical analysis of miRNA expressions, which can give insights to improve the classifier's performance. The method implemented in the package was first introduced in L. Ricci, V. Del Vescovo, C. Cantaloni, M. Grasso, M. Barbareschi and M. A. Denti, "Statistical analysis of a Bayesian classifier based on the expression of miRNAs", BMC Bioinformatics 16:287, 2015 <doi:10.1186/s12859-015-0715-9>. The package is thoroughly described in M. Castelluzzo, A. Perinelli, S. Detassis, M. A. Denti and L. Ricci, "MiRNA-QC-and-Diagnosis: An R package for diagnosis based on MiRNA expression", SoftwareX 12:100569, 2020 <doi:10.1016/j.softx.2020.100569>. Please cite both these works if you use the package for your analysis. DISCLAIMER: The software in this package is for general research purposes only and is thus provided WITHOUT ANY WARRANTY. It is NOT intended to form the basis of clinical decisions. Please refer to the GNU General Public License 3.0 (GPLv3) for further information.

README

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## PACKAGE EXAMPLES ##
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# Synthetic examples
This folder contains two synthetic datasets, synthetic_dataset_alpha.dat and synthetic_dataset_beta.dat
	synthetic_dataset_alpha.dat is a training set, thus having a 'Class' column.
	synthetic_dataset_beta.dat is a set to be classified, and therefore the 'Class' column is absent.
The pipeline in the script 'example_synthetic_dataset.R' exploits these datasets to show how to use the package functions.
The examples reported in 'example_synthetic_dataset.R' are discussed in more details within the user manual.

# Real data examples
This folder contains two experimental datasets, each one divided into a training set and a test set:
	real_dataset_1_training.dat, real_dataset_1_testing.dat real_dataset_1_additional.dat
		These two files contain a first dataset, which was part of the following work:
		L. Ricci et al., "Statistical analysis of a Bayesian classifier based on the expression of miRNAs", BMC Bioinformatics 16:287 (2015) DOI:10.1186/s12859-015-0715-9
		The dataset was published alongside this work as Supplementary Material and can be downloaded at the following URL:
		https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-015-0715-9/MediaObjects/12859_2015_715_MOESM1_ESM.txt

	real_dataset_2_training.dat, real_dataset_2_testing.dat
		These two files contain the second dataset, which was part of the following work:
		S. Detassis et al., "miR375-3p Distinguishes Low-Grade Neuroendocrine From Non-neuroendocrine Lung Tumors in FFPE Samples", Frontiers in Molecular Biosciences 7:86 (2020) DOI:10.3389/fmolb.2020.00086
		The dataset was submitted to the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and is waiting for approval.
		The corresponding URL will be added to this README file as soon as it is available.
Two example scripts, 'example_real_dataset_1.R' and 'example_real_dataset_2.R', provide pipelines that analyze these data.

# Other files
Files whose name starts with "test_" are related to post-install tests of the package and can be ignored.

Versions across snapshots

VersionRepositoryFileSize
1.1.3 rolling linux/jammy R-4.5 MiRNAQCD_1.1.3.tar.gz 594.1 KiB
1.1.3 rolling linux/noble R-4.5 MiRNAQCD_1.1.3.tar.gz 594.0 KiB
1.1.3 rolling source/ R- MiRNAQCD_1.1.3.tar.gz 534.0 KiB
1.1.3 latest linux/jammy R-4.5 MiRNAQCD_1.1.3.tar.gz 594.1 KiB
1.1.3 latest linux/noble R-4.5 MiRNAQCD_1.1.3.tar.gz 594.0 KiB
1.1.3 latest source/ R- MiRNAQCD_1.1.3.tar.gz 534.0 KiB
1.1.3 2026-04-26 source/ R- MiRNAQCD_1.1.3.tar.gz 534.0 KiB
1.1.3 2026-04-23 source/ R- MiRNAQCD_1.1.3.tar.gz 534.0 KiB
1.1.3 2026-04-09 windows/windows R-4.5 MiRNAQCD_1.1.3.zip 605.3 KiB
1.1.3 2025-04-20 source/ R- MiRNAQCD_1.1.3.tar.gz 534.0 KiB

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