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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.
Proper citation: PyRosetta (RRID:SCR_018541) 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
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
http://web.cmb.usc.edu/people/alber/Software/tomominer/
Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.
Proper citation: TomoMiner (RRID:SCR_015045) Copy
https://github.com/Rinoahu/SwiftOrtho
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Proper citation: SwiftOrtho (RRID:SCR_017122) Copy
https://github.com/dodomorandi/hatspil
Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability.
Proper citation: HaTSPiL (RRID:SCR_017059) Copy
https://github.com/g2-bernotas/PS-Plant-Framework
Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters.
Proper citation: PS-Plant Framework (RRID:SCR_017032) Copy
https://github.com/mandricigor/ScaffMatch
Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.
Proper citation: ScaffMatch (RRID:SCR_017025) Copy
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