Related papers: Analysing high-throughput sequencing data in Pytho…
High-throughput sequencing file formats and tools encode coordinate intervals with respect to a reference sequence in at least four distinct, incompatible ways. Integrating data from and moving data between different formats has the…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analysing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data -- such as fluorescence brightness, lifetime, and…
Since its launch, TESS has provided high cadence observations for objects across the sky. Although high cadence TESS observations provide a unique possibility to study the rapid time evolution of numerous objects, artifacts in the data make…
The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
$\textbf{Motivation:}$ Hierarchical data structures are prevalent across several fields of research, as they represent an organised and efficient approach to study complex interconnected systems. Their significance is particularly evident…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Summary: Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming increasing routine for monitoring changes in the structural dynamics of proteins. Differential HDX-MS allows comparison of individual protein states, such as in the…
Data engineering is becoming an increasingly important part of scientific discoveries with the adoption of deep learning and machine learning. Data engineering deals with a variety of data formats, storage, data extraction, transformation,…
In this paper, we present MusPy, an open source Python library for symbolic music generation. MusPy provides easy-to-use tools for essential components in a music generation system, including dataset management, data I/O, data preprocessing…
We present SPEAR, an open-source python library for data programming with semi supervision. The package implements several recent data programming approaches including facility to programmatically label and build training data. SPEAR…
In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden…
Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Text-to-SQL, the task of translating natural language questions into SQL queries, plays a crucial role in enabling non-experts to interact with databases. While recent advancements in large language models (LLMs) have significantly enhanced…
Over the past decade, the Python-based Simulations of Chemistry Framework (PySCF) has developed into a widely used open-source platform for electronic structure theory and quantum chemical method development. This article reviews the major…
As high-throughput sequencing has become common practice, the cost of sequencing large amounts of genetic data has been drastically reduced, leading to much larger data sets for analysis. One important task is to identify biological…
HOTTBOX is a Python library for exploratory analysis and visualisation of multi-dimensional arrays of data, also known as tensors. The library includes methods ranging from standard multi-way operations and data manipulation through to…
The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…