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Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
Proper citation: NetworkX (RRID:SCR_016864) Copy
https://github.com/maypoleflyn/BSATOS
Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.
Proper citation: Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) Copy
Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases.
Proper citation: Allen Brain Atlas (RRID:SCR_017001) Copy
https://github.com/BlaisProteomics/mzStudio
Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows.
Proper citation: mzStudio (RRID:SCR_017088) Copy
https://github.com/schatzlab/genomescope
Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach.
Proper citation: GenomeScope (RRID:SCR_017014) Copy
https://omicssimla.sourceforge.io
Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.
Proper citation: OmicsSIMLA (RRID:SCR_017011) Copy
http://sehilyi.com/mirtarvisplus/
Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data.
Proper citation: miRTarVisPlus (RRID:SCR_017103) Copy
https://CRAN.R-project.org/package=tidyr
Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data.
Proper citation: tidyr (RRID:SCR_017102) Copy
https://github.com/FeeLab/seqNMF
Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers.
Proper citation: seqNMF (RRID:SCR_017068) Copy
Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE.
Proper citation: iMicrobe (RRID:SCR_017108) Copy
https://www.datasci.com/products/software/ponemah
Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming.
Proper citation: Ponemah (RRID:SCR_017107) Copy
https://www.cdc.gov/diseasesconditions/index.html
List of diseases and conditions on Centers for Disease Control and Prevention website., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CDC Diseases & Conditions (RRID:SCR_017070) Copy
Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.
Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy
Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.
Proper citation: BSA4Yeast (RRID:SCR_017113) Copy
https://github.com/tseemann/shovill
Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.
Proper citation: shovill (RRID:SCR_017077) Copy
https://inutano.github.io/cwl-metrics/
Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux.
Proper citation: cwl-metrics (RRID:SCR_017076) Copy
https://github.com/PGB-LIV/VAPPER
Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.
Proper citation: VAPPER (RRID:SCR_016993) Copy
https://github.com/CGATOxford/UMI-tools
Open source software package for handling Unique Molecular Identifiers in NGS data sets.
Proper citation: UMI-tools (RRID:SCR_017048) Copy
http://cab.spbu.ru/software/rnaspades/
Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9.
Proper citation: rnaSPAdes (RRID:SCR_016992) Copy
https://github.com/dgrun/RaceID
Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.
Proper citation: RaceID (RRID:SCR_017045) Copy
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