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Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.
Proper citation: CajaDB (RRID:SCR_016506) Copy
https://www.genome.jp/tools/dinies/
Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.
Proper citation: DINIES (RRID:SCR_016505) Copy
https://gitlab.com/vtraver/PNNsMiceMachineVision
Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective".
Proper citation: PNNsMiceMachineVision (RRID:SCR_016485) Copy
http://www.flywings.org.uk/morphoj_page.htm
Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data.
Proper citation: MorphoJ (RRID:SCR_016483) Copy
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000363.v16.p10
Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation.
Proper citation: SABRe CVD Initiative (RRID:SCR_016572) Copy
https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf
Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.
Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy
https://github.com/WGS-TB/MentaLiST
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Proper citation: MentaLiST (RRID:SCR_016469) Copy
Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Proper citation: cisTEM (RRID:SCR_016502) Copy
https://sourceforge.net/p/iris-scanning/calliope
Software package for image processing for MATLAB. Used for processing of calcium imaging data.
Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy
https://cumulus.readthedocs.io/en/stable
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Proper citation: Cumulus (RRID:SCR_021644) Copy
Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.
Proper citation: Stan (RRID:SCR_018459) Copy
http://www.nitrc.org/projects/reprocontainers/
Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.
Proper citation: ReproNim/containers (RRID:SCR_018467) Copy
https://bioconductor.org/packages/ggtree/
Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.
Proper citation: ggtree (RRID:SCR_018560) Copy
http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx
Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.
Proper citation: DAMBE (RRID:SCR_018528) Copy
https://github.com/lmb-embrapa/machado
Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.
Proper citation: Machado (RRID:SCR_018428) Copy
https://github.com/OHDSI/CohortMethod
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Proper citation: CohortMethod (RRID:SCR_018511) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
http://tools.dice-database.org/GOnet/)
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Proper citation: GOnet (RRID:SCR_018977) Copy
http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/
Software Matlab toolbox to perform representational similarity analysis for neural data.
Proper citation: Toolbox for Representational Similarity Analysis (RRID:SCR_019029) Copy
https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation
Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer.
Proper citation: CLIP Tool Kit (RRID:SCR_019034) Copy
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