Related papers: cellanneal: A User-Friendly Deconvolution Software…
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…
Seglearn is an open-source python package for machine learning time series or sequences using a sliding window segmentation approach. The implementation provides a flexible pipeline for tackling classification, regression, and forecasting…
PyUnfold is a Python package for incorporating imperfections of the measurement process into a data analysis pipeline. In an ideal world, we would have access to the perfect detector: an apparatus that makes no error in measuring a desired…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
This paper presents the philosophy, design and feature-set of Neural Network Distiller, an open-source Python package for DNN compression research. Distiller is a library of DNN compression algorithms implementations, with tools, tutorials…
We describe a software toolbox for the configuration of deep neural networks in the domain of skin cancer classification. The implemented software architecture allows developers to quickly set up new convolutional neural network (CNN)…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully…
Even though in recent years the scale of statistical analysis problems has increased tremendously, many statistical software tools are still limited to single-node computations. However, statistical analyses are largely based on dense…
Spectropolarimetry, the observation of polarization and intensity as a function of wavelength, is a powerful tool in stellar astrophysics. It is particularly useful for characterizing stars and circumstellar material, and for tracing the…
We present the Python package CELL, which provides a modular approach to the cluster expansion (CE) method. CELL can treat a wide variety of substitutional systems, including one-, two-, and three-dimensional alloys, in a general…
It is critical to accurately simulate data when employing Monte Carlo techniques and evaluating statistical methodology. Measurements are often correlated and high dimensional in this era of big data, such as data obtained in…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
We implement Ananke: an object-oriented Python package for causal inference with graphical models. At the top of our inheritance structure is an easily extensible Graph class that provides an interface to several broadly useful graph-based…
Ordinal data is widely prevalent in clinical and other domains, yet there is a lack of both modern, machine-learning based methods and publicly available software to address it. In this paper, we present a model-agnostic method of ordinal…
This paper describes a novel Python package, named causalgraph, for modeling and saving causal graphs embedded in knowledge graphs. The package has been designed to provide an interface between causal disciplines such as causal discovery…
SUMMARY : We developed a user-friendly software to generate synthetic confocal microscopy images from a ground truth specified as a 3D bitmap with pixels of arbitrary size. The software can analyze a real confocal stack to derivate noise…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…