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http://www.genepath.org/

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. GenePath uses abductive inference to elucidate network constraints and logic to derive consistent networks. Typically, it starts with a set of genetic experiments, uses a set of embedded rules (patterns) to infer relations between genes and outcome, and based on these relations constructs a genetic network.

Proper citation: GenePath (RRID:SCR_007974) Copy   

•   Source: SciCrunch Registry

https://epd.expasy.org/epd/

EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters.

Proper citation: EPDnew (RRID:SCR_002485) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/unigene

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Proper citation: UniGene (RRID:SCR_004405) Copy   

•   Source: SciCrunch Registry

https://github.com/zhenzonglei/abat

Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.

Proper citation: Allen Brain Atlas Tools (RRID:SCR_023855) Copy   

•   Source: SciCrunch Registry

https://www.earthcube.org

Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science.

Proper citation: EarthCube (RRID:SCR_024576) Copy   

•   Source: SciCrunch Registry

https://californiacoastalatlas.net/

Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes.

Proper citation: California Coastal Atlas (RRID:SCR_024554) Copy   

•   Source: SciCrunch Registry

https://www.cernerenviza.com/syndicated-insights-and-reports-for-life-sciences/cancermpact

American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases.

Proper citation: Cerner Enviza (RRID:SCR_024435) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/SCENIC

Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data.

Proper citation: SCENIC (RRID:SCR_017247) Copy   

•   Source: SciCrunch Registry

https://it.uib.no/en/Safe

Platform for Secure Access to Research Data and E-Infrastructure based on European Standards for Health Case information. Used for secure processing of sensitive personal data in research in health and care sector.

Proper citation: Secure Access to Research Data and E-Infrastructure (RRID:SCR_017246) Copy   

•   Source: SciCrunch Registry

https://sciex.com/products/software/lipidview-software

Software tool for molecular characterization and quantification of lipid species from electrospray mass spectrometry data. Enables lipid profiling by searching parent and fragment ion masses against lipid fragment database and reports numerical and graphical output for various lipid molecular species, lipid classes, fatty acids, and long chain bases.

Proper citation: LipidView Software (RRID:SCR_017003) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/KHanghoj/DamMet

Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.

Proper citation: DamMet (RRID:SCR_016959) Copy   

•   Source: SciCrunch Registry

https://osf.io/rmqaw/

Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control.

Proper citation: stop-signal task resources (RRID:SCR_017137) Copy   

•   Source: SciCrunch Registry

https://github.com/bids-standard/bids-validator

Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure.

Proper citation: BIDS Validator (RRID:SCR_017255) Copy   

•   Source: SciCrunch Registry

https://hub.docker.com/r/mziemann/tallyup/

Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript.

Proper citation: Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) Copy   

•   Source: SciCrunch Registry

http://ophid.utoronto.ca/mirDIP/

microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies.

Proper citation: mirDIP (RRID:SCR_016770) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/maestro

Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.

Proper citation: Maestro (RRID:SCR_016748) Copy   

•   Source: SciCrunch Registry

http://cab.spbu.ru/software/rnaquast/

Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software.

Proper citation: rnaQUAST (RRID:SCR_016994) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/brainlife_io/

Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.

Proper citation: brainlife.io (RRID:SCR_016513) Copy   

•   Source: SciCrunch Registry

https://github.com/ropenscilabs/datastorr

Software package for simple data retrieval and versioning.

Proper citation: datastorr (RRID:SCR_017040) Copy   

•   Source: SciCrunch Registry

https://openknowledgemaps.org/

Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge.

Proper citation: Open Knowledge Maps (RRID:SCR_016470) Copy   

•   Source: SciCrunch Registry