13 papers · ranked by Valyu relevance
Vladislav Myrov, Felix Siebenhühner, Sheng H Wang, Gabriele Arnulfo + 8 more
‘CROCOpy’ is a light-weighted toolbox for the assessment of neuronal oscillations, and multiple observables of functional connectivity (phase synchronization, amplitude coupling, and cross-frequency coupling) and critical dynamics (avalanches, long-range temporal correlations, bistability, and functional…
Ido Haber, Aksel Jackson, Axel Thielscher, Aviad Hai + 1 more
Temporal interference stimulation is a novel non-invasive brain stimulation approach that promises selective targeting of deep brain structures while minimizing off-target cortical stimulation. Despite a growing interest in temporal interference applications, there is a need for integrated computational tools that…
Simone Coppola, Séamus Holden
Detection of morphological phenotypes from light microscopy is a key part of microbiology. Despite advances in automated morphological analysis, accurate measurements still often require significant user input. To address this, we have developed micromorph, a Python package to measure bacterial morphological properties…
Annie G. Bryant
Recent years have seen an expanding repertoire of code-based tools for visualizing neuroimaging data, promoting reproducibility and interpretability of brain-mapping findings. However, most open-source visualization packages for the human brain are geared toward the cerebral cortex, and the comparatively few options…
Alexander Fengler, Yang Xu, Krishn Bera, Carlos Paniagua + 2 more
Computational models are central to cognitive neuroscience, but their rigorous application to experimental datasets is often constrained to a narrow set of canonical models that afford tractable analytical computations. We introduce the HSSM (Hierarchical Sequential Sampling Model) ecosystem, a Python toolbox that…
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…
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…
V. Chiara, A. Buatois, S.-Y. Kim
Video-tracking programs have now become an essential tool for researchers measuring animal behavior across biological fields. The panel of available programs is growing rapidly, providing researchers with numerous specific tools that will match their precise needs. However, their proliferation may complicate…
Amirhossein Khalilian-Gourtani, Yasamin Esmaeili, Andrew J. Michalak, Adeen Flinker
Intracranial electrophysiological recordings, including electrocorticography (ECoG) and stereo-EEG (sEEG), are increasingly used across research programs to study human brain function due to their high spatiotemporal resolution. Numerous tools exist for electrode localization and visualization; however, most focus on…
Yonatan Sanz Perl, Jakub Vohryzek, Anira Escrichs, Morten L. Kringelbach + 1 more
Brain disorders remain one of the greatest challenges in neuroscience. Computational precision medicine offers a promising framework to reveal the mechanistic principles governing both healthy and pathological brain dynamics. In this context, we present The Turbulent Brain (TTB) toolbox, an open-source MATLAB platform…
Bernard C. Wang, Raymond Gifford, Nathan C. L. Kong, Feng Ruan + 2 more
MatClassRSA is a MATLAB toolbox that performs magnetoen-cephalography and electroencephalography (M/EEG) classification and other analyses related to Representational Similarity Analysis (RSA). The toolbox is designed for cognitive neuroscience researchers who wish to perform classification-based decoding analyses of…
P. Travis Thompson, Hunter N.B. Moseley
The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved; updating its mwTab and JSON…
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…