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https://neurophysics.ucsd.edu/software.php
Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego.
Proper citation: UltraMegaSort 2000 (RRID:SCR_015857) Copy
http://users.sussex.ac.uk/~lionelb/MVGC/
Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions.
Proper citation: MVGC Multivariate Granger Causality Matlab Toolbox (RRID:SCR_015755) Copy
https://sourceforge.net/projects/icacompass/
Algorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP.
Proper citation: COMPASS (RRID:SCR_015874) Copy
http://download.ant-neuro.com/matlab/
Software as an EEGLAB tool used for LIBEEP recordings.
Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy
http://cns.hkbu.edu.hk/RIDE.htm
Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.
Proper citation: Residue Iteration Decomposition (RRID:SCR_022174) Copy
https://github.com/MMTI/Toolkit_for_MIRA_LAB_Striatal_Segmentation
Software MATLAB pipeline that produces CNN-based segmentations of striatal regions of brain based on structural T1w image.
Proper citation: Toolkit for MIRA LAB Striatal Segmentation (RRID:SCR_023073) Copy
https://github.com/lucadellasantina/ObjectFinder
Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes.
Proper citation: ObjectFinder (RRID:SCR_023319) Copy
https://github.com/howisonlab/softcite-dataset
Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
Proper citation: SoftCite (RRID:SCR_024411) Copy
http://collaborations.gis.a-star.edu.sg/~cmb6/TherMos/
Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TherMos (RRID:SCR_002790) Copy
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