Related papers: genomepy: genes and genomes at your fingertips

We introduce FDApy, an open-source Python package for the analysis of functional data. The package provides tools for the representation of (multivariate) functional data defined on different dimensional domains and for functional data that…

Background: The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing…

High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient…

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach…

Gammapy is a Python package for high-level gamma-ray data analysis built on Numpy, Scipy and Astropy. It enables us to analyze gamma-ray data and to create sky images, spectra and lightcurves, from event lists and instrument response…

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…

BayesPy is an open-source Python software package for performing variational Bayesian inference. It is based on the variational message passing framework and supports conjugate exponential family models. By removing the tedious task of…

We present Globalping, an open-source, community-driven platform for scalable, real-time global network measurements. It democratizes access to network diagnostics by offering every user, including non-technicals, technicals, and companies,…

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…

In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…

Individual-level data (microdata) that characterizes a population, is essential for studying many real-world problems. However, acquiring such data is not straightforward due to cost and privacy constraints, and access is often limited to…

We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…

Considerable scientific work involves locating, analyzing, systematizing, and synthesizing other publications. Its results end up in a paper's "background" section or in standalone articles, which include meta-analyses and systematic…

In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…

Public repositories for genome and proteome annotations, such as the Gene Ontology (GO), rarely stores negative annotations, i.e. proteins not possessing a given function. This leaves undefined or ill defined the set of negative examples,…

This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to…

Genetic data are now routinely used to study the history of population size, subdivision, and gene flow. A variety of formal statistical methods is available for testing hypotheses and fitting models to data. Yet it is often unclear which…

The Italian AGILE space mission, with its Gamma-Ray Imaging Detector (GRID) instrument sensitive in the 30 MeV-50 GeV gamma-ray energy band, has been operating since 2007. Agilepy is an open-source Python package to analyse AGILE/GRID data.…