Related papers: PyamilySeq: A Python Tool for Interpretable Gene (…
Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…
Radiomics enables the extraction of quantitative biomarkers from medical images for precision modeling, but reproducibility and scalability remain limited due to heterogeneous software implementations and incomplete adherence to standards.…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
In recent years, advances in high throughput sequencing technology have led to a need for specialized methods for the analysis of digital gene expression data. While gene expression data measured on a microarray take on continuous values…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
The identification of groups' prototypes, i.e. elements of a dataset that represent different groups of data points, may be relevant to the tasks of clustering, classification and mixture modeling. The R package pivmet presented in this…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Pyxel is a novel python tool for end-to-end detection chain simulation i.e. from detector optical effects to readout electronics effects. It is an easy-to-use framework to host and pipeline any detector effect model. It is suited for…
Large-scale single-cell and Perturb-seq investigations routinely involve clustering cells and subsequently annotating each cluster with Gene-Ontology (GO) terms to elucidate the underlying biological programs. However, both stages,…
We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data…
In this paper, we present pyspect, a Python toolbox that simplifies the use of reachability analysis for temporal logic problems. Currently, satisfying complex requirements in cyber-physical systems requires significant manual effort and…
Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…
Malicious Python packages make software supply chains vulnerable by exploiting trust in open-source repositories like Python Package Index (PyPI). Lack of real-time behavioral monitoring makes metadata inspection and static code analysis…
Objective: Data clustering is a common exploration step in the omics era, notably in genomics and proteomics where many genes or proteins can bequantified from one or more experiments. Bayesian clustering is a powerful algorithm that can…
The exponential growth of complex data demands fully automatic clustering. Gaussian mixture models (GMMs) provide uncertainty-aware grouping but often require expertise to specify hyperparameters, e.g., component count and covariance…
Galaxy morphological classification is a fundamental aspect of galaxy formation and evolution studies. Various machine learning tools have been developed for automated pipeline analysis of large-scale surveys, enabling a fast search for…
PiML (read $\pi$-ML, /`pai`em`el/) is an integrated and open-access Python toolbox for interpretable machine learning model development and model diagnostics. It is designed with machine learning workflows in both low-code and high-code…
We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data…