Related papers: Analysing high-throughput sequencing data in Pytho…
Gene expression profiling provides profound insights into molecular mechanisms, but its time-consuming and costly nature often presents significant challenges. In contrast, whole-slide hematoxylin and eosin (H&E) stained histological images…
PypeIt is a Python package for semi-automated reduction of astronomical, spectroscopic data. Its algorithms build on decades-long development of previous data reduction pipelines by the developers (Bernstein, Burles, & Prochaska, 2015;…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…
RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…
We present the open-source image processing software package PySAP (Python Sparse data Analysis Package) developed for the COmpressed Sensing for Magnetic resonance Imaging and Cosmology (COSMIC) project. This package provides a set of…
Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression estimation requires a probabilistic approach to properly…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…
Tensors are higher-order extensions of matrices. While matrix methods form the cornerstone of machine learning and data analysis, tensor methods have been gaining increasing traction. However, software support for tensor operations is not…
Computer algebra systems play an important role in science as they facilitate the development of new theoretical models. The resulting symbolic equations are often implemented in a compiled programming language in order to provide fast and…
Two-sample hypothesis testing for network comparison presents many significant challenges, including: leveraging repeated network observations and known node registration, but without requiring them to operate; relaxing strong structural…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
Rules offer an invaluable combination of predictive and descriptive capabilities. Our package for rule-based data analysis, RuleKit, has proven its effectiveness in classification, regression, and survival problems. Here we present its…
This paper describes the PySLHA package, a Python language module and program collection for reading, writing and visualising SUSY model data in the SLHA format. PySLHA can read and write SLHA data in a very general way, including the…
Statistical methods for genomewide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software.…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
Machine learning is an important tool for analyzing high-dimension hyperspectral data; however, existing software solutions are either closed-source or inextensible research products. In this paper, we present cuvis.ai, an open-source and…
We present PrismSSL, a Python library that unifies state-of-the-art self-supervised learning (SSL) methods across audio, vision, graphs, and cross-modal settings in a single, modular codebase. The goal of the demo is to show how researchers…
Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…