13 papers · ranked by Valyu relevance
Sebastien Ravel, Nina Marthe, Camille Carrette, Mourdas Mohamed + 2 more
Pangenome variation graphs (PVGs), which represent genomic diversity through multiple genomes alignment, are powerful tools for studying genomic variations in populations. However, current tools often lack integration, efficiency, or require format conversions, to use them, hindering their usability. Here, we introduce…
K. Tsolakidis, Artu Breuer, S. Bender, Stavroula Margaritaki + 3 more
Advances in fluorescence microscopy have dramatically expanded the range of biological questions that can be addressed, enabling quantitative observations of molecular interactions and cellular dynamics with unprecedented spatial and temporal resolution. However, the growing complexity of imaging data has outpaced our…
Endre Bakken Stovner, Max Ticó, Ester Muñoz del Campo, Joan Pallarès-Albanell + 3 more
Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice intervals), enabling the intuitive development of efficient pipelines for diverse sequence data, including gene annotations…
Jayadev Joshi, Fabio Cumbo, Daniel Blankenberg
R is widely used in statistical computing, data analysis, and bioinformatics. A key contributor to its success in bioinformatics and computational biology is the open-source project Bioconductor. As of its latest release (3.20), the Bioconductor community offers 2,289 software packages for biomedical research…
Julien Barnier, Cassandra Bompard, Aurélie Siberchicot, Vincent Navratil + 2 more
The need to visualize data associated with NCBI Taxonomy Identifiers (taxids) is growing in various biological fields ranging from comparative genomics to metagenomics and metabarcoding, and even for outreach. No tool today allows to visualize such data while still keeping the full vision of the whole taxonomy…
Tatsat Banerjee, Bedri Abubaker-Sharif, Peter N. Devreotes, Pablo A. Iglesias
The plasma membrane and accompanying cortex serve as one of the major hubs of the signal transduction and cytoskeletal activities that collectively regulate numerous cell physiological processes such as migration, polarity, macropinocytosis, phagocytosis, cytokinesis, etc. Yet, dynamically tracking membrane-cortex…
Melissa L. Blotter, Jacob Cahoon, Jacob H. Norby, Katelyn C. Forbes + 4 more
High-density multi-electrode arrays (HD-MEAs) generate large, complex datasets that are challenging to efficiently manage and analyze with existing tools, especially in open-source environments. To address this, we developed the BYU Seizure and Analytics Tool (YSA), an open-source graphical user interface (GUI) built…
James A. London, Abhishek K. Singh, Teague C. Svendsen, Naciye Esma Tirtom + 2 more
Magnetic tweezers are a popular biophysical instrument for manipulating and measuring single molecules. Most groups rely on custom-built setups tailored to specific experiments, making it challenging to implement and share software. Typically, image acquisition and hardware control are automated via LabVIEW, while…
JF Mulvey
pylimma is a faithful Python port of limma, intended to bring one of the most widely used tools for differential expression analysis to the developing Python ecosystem for transcriptomics and proteomics. We validated pylimma against the existing R implementation through 227 function-level comparisons and across six…
Mohamed Salim Nasser Al Hinai, Zakira Naureen, Syed Abdullah Gilani
Since, Bioinformatic research is getting attraction that can be seen with sudden increase in development of tools as well as publications. However, there are challenges in bioinformatics which are making the results difficult to obtain while facing reproducibility, scalability, and accessibility of computational…
Conrad Oakes, Vera Beilinson, Margaret J. McFall-Ngai, Lior Pachter
Bacteria are highly heterogeneous, even under controlled conditions, making single-cell RNA sequencing (scRNA-seq) essential for studying microbial diversity and symbiosis. Since its first application in 2015, bacterial scRNA-seq has expanded, but different assays depend on distinct, custom, inhouse pre-processing…
Marie Anselmet, Laura Xénard, Marvin Albert, Rodrigo Arias-Cartin + 14 more
Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, Microbiologists are confronted with numerous algorithms that must be carefully chosen and parameterized to achieve…
Jakob Schuster, Kathleen Zeglinski, Lucinda Xiao, Olivia Voulgaris + 5 more
The wide variety of protocols and applications for DNA and RNA sequencing makes flexible tools for read processing an important step in sequence analysis. Beyond trimming and demultiplexing, custom read-level processing is commonly required for data exploration, QC and analysis. Existing tools are often task-specific…