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https://github.com/Kingsford-Group/kourami

Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.

Proper citation: Kourami (RRID:SCR_022280) Copy   

•   Source: SciCrunch Registry

https://opencell.czbiohub.org/

Proteome scale collection of protein localization and interaction measurements in human cells. Proteome scale endogenous tagging enables cartography of human cellular organization.

Proper citation: OpenCell (RRID:SCR_021870) Copy   

•   Source: SciCrunch Registry

https://isamplesorg.github.io/home/

Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.

Proper citation: iSamples (RRID:SCR_021750) Copy   

•   Source: SciCrunch Registry

https://github.com/RabadanLab/arcasHLA

Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.

Proper citation: arcasHLA (RRID:SCR_022286) Copy   

•   Source: SciCrunch Registry

https://www.kbase.us/

Data science platform for predicting and designing biological function. Platform to model plant and microbial physiology and community dynamics. Knowledge creation and discovery environment for biologists and bioinformaticians. Integrates variety of data and analysis tools from US Department of Energy and other public services into platform that leverages scalable computing infrastructure and performs systems biology analyses. Enables scientists to analyze their own data within context of public data and share findings across system.

Proper citation: KBase (RRID:SCR_022162) Copy   

•   Source: SciCrunch Registry

https://ccsp.hms.harvard.edu/

Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium.

Proper citation: Harvard Medical School Center for Cancer Systems Pharmacology (RRID:SCR_022831) Copy   

•   Source: SciCrunch Registry

https://www.turing.ac.uk/research/research-projects/turing-way-handbook-reproducible-data-science

Guide to reproducible data science to support students and academics as they develop their code, with aim of helping them produce work that will be regarded as gold standard examples of trustworthy and reusable research. Include training material on version control, analysis testing and open and transparent communication with future users.

Proper citation: Turing Way handbook for reproducible data science (RRID:SCR_021908) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rascaf

Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data.

Proper citation: Rascaf (RRID:SCR_022014) Copy   

•   Source: SciCrunch Registry

https://finngen.gitbook.io/documentation/

Public private partnership combining genotype data from Finnish biobanks and digital health record data from Finnish health registries. Provides opportunity to study genetic variation in relation to disease trajectories in isolated population.

Proper citation: FinnGen (RRID:SCR_022254) Copy   

•   Source: SciCrunch Registry

https://www.fdilab.org/toolsservices

Integrated data set and analytics platform combining Research Resource Identifiers (RRIDs), text mining and data aggregation.

Proper citation: Resource Information Network (RRID:SCR_023186) Copy   

•   Source: SciCrunch Registry

http://meadows-research.com

Online behavioral experiment platform.

Proper citation: Meadows (RRID:SCR_023218) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/ratcave/

Portal provides open source, cross platform Python library that adds 3D stimulus support to all OpenGL based 2D Python stimulus libraries. Ratcave comes with resources including basic 3D object primitives and wide range of 3D light effects. Intuitive object oriented interface allows for all objects, which include meshes, lights, and cameras, can be repositioned, rotated, and scaled.

Proper citation: Ratcave project (RRID:SCR_021555) Copy   

•   Source: SciCrunch Registry

https://app.pennsieve.io

Platform to manage and curate large scientific datasets. Used for scientific data management and analysis.Provides advanced functionality to organize files and complex metadata describing datasets and allows users to interact, search, and analyze these data through web application or programmatically using Python client. Provides end-to-end solution for publishing datasets through Blackfynn Discover, assigning DOIs and ensuring that published data becomes available to larger academic community in sustainable and FAIR manner.

Proper citation: Pennsieve Data Management Platform (RRID:SCR_021677) Copy   

•   Source: SciCrunch Registry

https://scijava.org/

Collection of foundational software libraries, upon which ImageJ2 and Fiji are built. It is a collaboration of projects providing software for scientific computing in effort to cooperate and reuse code.

Proper citation: scijava (RRID:SCR_023335) Copy   

•   Source: SciCrunch Registry

https://covidcg.org/?tab=home

Open browser to inform therapeutics development for tracking SARS-CoV-2 single nucleotide variations, lineages, and clades using virus genomes on GISAID database while filtering by location, date, gene, and mutation of interest. can Provides information on which virus mutations are present in area during specific period by processing data on mutations found in viral genetic material collected worldwide from hundreds of thousands of people with COVID-19, which are hosted in existing online database.

Proper citation: COVID CG (RRID:SCR_022266) Copy   

•   Source: SciCrunch Registry

https://sciendo.com/article/10.5617/jeb.2985

A software to display, record and data processing of physiological signals. DataLyser is custom-built software developed at Walter Reed Army Institute of Research, Silver Spring, MD. It is not copyrighted.

Proper citation: DataLyser (RRID:SCR_022783) Copy   

•   Source: SciCrunch Registry

https://github.com/wtsi-hpag/PretextMap

Software tool to convert SAM formatted read pairs into genome contact maps. Prepares alignments for visualization with PretextView.

Proper citation: PretextMap (RRID:SCR_022023) Copy   

•   Source: SciCrunch Registry

https://www.openanatomy.org/

Project aims to change anatomy atlas by building atlases through open data, community based collaborative development, and free distribution of medical knowledge. Provides access to several 2D and 3D browser based tools.

Proper citation: Open Anatomy Project (RRID:SCR_022141) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/PlantGenomicsLab/gFACs

Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis.

Proper citation: gFACs (RRID:SCR_022017) Copy   

•   Source: SciCrunch Registry

https://www.childrensmercy.org/childrens-mercy-research-institute/studies-and-trials/genomic-answers-for-kids/

Flagship initiative of Childrens Mercy Research Institute and Genomic Medicine Center in Kansas City. This research program is building pediatric data repository to facilitate search for answers and novel treatments.Goal is to collect genomic data and health information for 30,000 children and their families to create a database of genomes.

Proper citation: Genomic Answers for Kids (RRID:SCR_021840) Copy   

•   Source: SciCrunch Registry