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https://edspace.american.edu/openbehavior/project/pavca/
Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.
Proper citation: PavCA project (RRID:SCR_022508) Copy
http://hollywood.mit.edu/exonscan/
Software framework for modeling sequence motifs based on maximum entropy principle.
Proper citation: ExonScan Web Server (RRID:SCR_022516) Copy
https://github.com/SGDDNB/ShinyCell
Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data.
Proper citation: ShinyCell (RRID:SCR_022756) Copy
Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system.
Proper citation: FreeStyle 1.8 SP1 (RRID:SCR_022877) Copy
https://github.com/LINCellularNeuroscience/VAME
Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.
Proper citation: Variational Embedding of Animal Motion (RRID:SCR_022477) Copy
https://CRAN.R-project.org/package=ComplexUpset
Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.
Proper citation: ComplexUpset (RRID:SCR_022752) Copy
Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.
Proper citation: ZDOCK Server (RRID:SCR_022518) Copy
https://github.com/Gaius-Augustus/learnMSA
Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.
Proper citation: learnMSA (RRID:SCR_022572) Copy
https://github.com/FunctionLab/sei-framework
Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.
Proper citation: sei (RRID:SCR_022571) Copy
https://github.com/djamesbarker/pMAT
Open source software suite for analysis of fiber photometry data.
Proper citation: pMAT (RRID:SCR_022570) Copy
https://github.com/JinmiaoChenLab/Rphenograph
Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.
Proper citation: Rphenograph (RRID:SCR_022603) Copy
https://www.ibm.com/products/structural-equation-modeling-sem
Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance.
Proper citation: IBM SPSS Amos (RRID:SCR_022686) Copy
https://www.erim.eur.nl/research-support/meta-essentials/
Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more.
Proper citation: Meta Essentials (RRID:SCR_022464) Copy
http://splicing.cs.washington.edu/
Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events.
Proper citation: Hexamer Additive Linear (RRID:SCR_022581) Copy
https://web.rniapps.net/netshift/
Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets.
Proper citation: NetShift (RRID:SCR_022733) Copy
Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.
Proper citation: UpSet (RRID:SCR_022731) Copy
http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/
Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.
Proper citation: VirtualPlant (RRID:SCR_022576) Copy
https://github.com/im3sanger/dndscv
Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies.
Proper citation: dNdScv (RRID:SCR_023123) Copy
https://biccn.org/teams/u01-fischl
Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex.
Proper citation: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) Copy
https://github.com/AlexandrovLab/SigProfilerExtractor/
Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample.
Proper citation: SigProfilerExtractor (RRID:SCR_023121) Copy
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