README.md

In sysbioTurin/connector: Fitting and clustering of longitudinal data

CONNECTOR

The transition from the evaluation of a single time point to the examination of the entire dynamic evolution of a system is possible only in the presence of the proper framework. The strong variability of dynamic evolution makes the definition of an explanatory procedure for data fitting and data clustering challenging. Here we present CONNECTOR, an R package able to analyze and inspect longitudinal data in a straightforward and revealing way, allowing the aggregation of time-series data through an unsupervised approach in informative clusters.

Link to a step by step guide in protocols.io .

Required installed packages

The following R packages must be installed to use connector: cowplot, fda, flexclust, ggplot2, MASS, Matrix, plyr, ggplotify, RColorBrewer, readxl, reshape2, splines, statmod, sfsmisc, shinyWidgets, viridis and dashboardthemes.

install.packages(c("cowplot", "fda", "flexclust", "ggplot2", "MASS", "Matrix", "plyr", "ggplotify",
    "RColorBrewer", "readxl", "reshape2", "splines", "statmod", "sfsmisc", "shinyWidgets", "viridis", "dashboardthemes"))

How to install connector

To install it you can use devtools:

install.packages("devtools")
library(devtools)
install_github("qBioTurin/connector", ref="master",dependencies=TRUE)

An example of connector analysis:

The MainCommandsList.R script contains the list of commands that can be used to reproduce the analysis described in the paper "CONNECTOR: fitting and clustering analysis of biological growth data".

To execute this script you can use demo()

library(connector)
demo("MainCommandsList", package = "connector")

Observe that some functions in the MainCommandsList.R script require several minutes to be terminated.

Diclaimer:

CONNECTOR developers have no liability for any use of docker4seq functions, including without limitation, any loss of data, incorrect results, or any costs, liabilities, or damages that result from the use of CONNECTOR.

How to cite

@article{pernice2023connector,
  title={CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system},
  author={Pernice, Simone and Sirovich, Roberta and Grassi, Elena and Viviani, Marco and Ferri, Martina and Sassi, Francesco and Alessandr{\`\i}, Luca and Tortarolo, Dora and Calogero, Raffaele A and Trusolino, Livio and others},
  journal={Bioinformatics},
  volume={39},
  number={5},
  pages={btad201},
  year={2023},
  publisher={Oxford University Press}
}

sysbioTurin/connector documentation built on April 9, 2024, 12:10 p.m.