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Register a new userMPAgenomics : An R package for multi-patients analysis of genomic markers
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MPAgenomics, standing for multi-patients analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation, and (ii) genomic marker selection from multi-patient copy number and SNP data profiles. It provides wrappers from commonly used packages to facilitate their repeated (sometimes difficult) use, offering an easy-to-use pipeline for beginners in R. The segmentation of successive multiple profiles (finding losses and gains) is based on a new automatic choice of influential parameters since default ones were misleading in the original packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given response.
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Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g., retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g., multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints in uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy. Availability: TRONCO is released under the GPL license, it is hosted in the Software section at http://bimib.disco.unimib.it/ and archived also at bioconductor.org. Contact: [email protected]
Alzheimers disease (AD) and Parkinsons disease (PD) are the two most common neurodegenerative disorders in humans. Because a significant percentage of patients have clinical and pathological features of both diseases, it has been hypothesized that the patho-cascades of the two diseases overlap. Despite this evidence, these two diseases are rarely studied in a joint manner. In this paper, we utilize clinical, imaging, genetic, and biospecimen features to cluster AD and PD patients into the same feature space. By training a machine learning classifier on the combined feature space, we predict the disease stage of patients two years after their baseline visits. We observed a considerable improvement in the prediction accuracy of Parkinsons dementia patients due to combined training on Alzheimers and Parkinsons patients, thereby affirming the claim that these two diseases can be jointly studied.
This paper introduces the R package sgmcmc; which can be used for Bayesian inference on problems with large datasets using stochastic gradient Markov chain Monte Carlo (SGMCMC). Traditional Markov chain Monte Carlo (MCMC) methods, such as Metropolis-Hastings, are known to run prohibitively slowly as the dataset size increases. SGMCMC solves this issue by only using a subset of data at each iteration. SGMCMC requires calculating gradients of the log likelihood and log priors, which can be time consuming and error prone to perform by hand. The sgmcmc package calculates these gradients itself using automatic differentiation, making the implementation of these methods much easier. To do this, the package uses the software library TensorFlow, which has a variety of statistical distributions and mathematical operations as standard, meaning a wide class of models can be built using this framework. SGMCMC has become widely adopted in the machine learning literature, but less so in the statistics community. We believe this may be partly due to lack of software; this package aims to bridge this gap.
This paper is dedicated to the R package FMM which implements a novel approach to describe rhythmic patterns in oscillatory signals. The frequency modulated Mobius (FMM) model is defined as a parametric signal plus a gaussian noise, where the signal can be described as a single or a sum of waves. The FMM approach is flexible enough to describe a great variety of rhythmic patterns. The FMM package includes all required functions to fit and explore single and multi-wave FMM models, as well as a restricted version that allows equality constraints between parameters representing a priori knowledge about the shape to be included. Moreover, the FMM package can generate synthetic data and visualize the results of the fitting process. The potential of this methodology is illustrated with examples of such biological oscillations as the circadian rhythm in gene expression, the electrical activity of the heartbeat and neuronal activity.
Process data refer to data recorded in the log files of computer-based items. These data, represented as timestamped action sequences, keep track of respondents response processes of solving the items. Process data analysis aims at enhancing educational assessment accuracy and serving other assessment purposes by utilizing the rich information contained in response processes. The R package ProcData presented in this article is designed to provide tools for processing, describing, and analyzing process data. We define an S3 class proc for organizing process data and extend generic methods summary and print for class proc. Two feature extraction methods for process data are implemented in the package for compressing information in the irregular response processes into regular numeric vectors. ProcData also provides functions for fitting and making predictions from a neural-network-based sequence model. These functions call relevant functions in package keras for constructing and training neural networks. In addition, several response process generators and a real dataset of response processes of the climate control item in the 2012 Programme for International Student Assessment are included in the package.
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