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https://github.com/smortezah/smashpp
Software tool to find and visualize rearrangements in DNA sequences.
Proper citation: smashpp (RRID:SCR_018307) 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
http://diana.imis.athena-innovation.gr/DianaTools
Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses.
Proper citation: DIANA Tools (RRID:SCR_018425) Copy
Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup.
Proper citation: GPS-SUMO (RRID:SCR_018261) Copy
https://www.flidea.tech/flic-support
R Code used to analyze FLIC data. Functions are provided to examine interactions with food for single well and food choice experiments when fly makes physical contact with liquid food.
Proper citation: R scripts for FLIC data analysis (RRID:SCR_018386) Copy
https://biit.cs.ut.ee/gprofiler/page/r
Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.
Proper citation: gProfiler2 (RRID:SCR_018190) Copy
Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction.
Proper citation: FlowPy (RRID:SCR_018195) Copy
https://www.kicnet.co.jp/solutions/biosignal/biosignal-2/vitalrecorder2/
Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video.
Proper citation: VitalRecorder2 (RRID:SCR_018199) Copy
https://www.fibl.org/en/themes/sustainability-assessment-info/sustainability-assessment-smart.html
Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners.
Proper citation: SMART-Farm Tool (RRID:SCR_018197) Copy
https://github.com/BGI-Qingdao/HAST
Software tool for partition stLFR reads based on trio binning using prenatally unique markers. Haplotype resolved assembly for synthetic long reads using Trio-Binning strategy.
Proper citation: HAST (RRID:SCR_018247) Copy
Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.
Proper citation: CuGenDB (RRID:SCR_018401) Copy
https://www.planmeca.com/software/
Software tool as 3D imaging software. Flexible and intuitive all-in-one dental software platform. Provides set of tools to meet imaging needs by any dental facility.
Proper citation: Planmeca Romexis (RRID:SCR_018403) Copy
Web tool implementing positional gene enrichment analysis of gene sets for high resolution identification of over represented chromosomal regions.
Proper citation: Positional Gene Enrichment (RRID:SCR_018360) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
https://github.com/bcgsc/NanoSim
Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software.
Proper citation: NanoSim (RRID:SCR_018243) Copy
https://github.com/grecolab/TinderMIX
Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features.
Proper citation: TinderMIX (RRID:SCR_018364) Copy
http://gpcr.biocomp.unibo.it/predgpi/pred.htm
Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes.
Proper citation: PredGPI (RRID:SCR_018363) Copy
http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi
Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.
Proper citation: STARANISO (RRID:SCR_018362) Copy
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
Web tool for conserved domains searching within protein or coding nucleotide sequence.
Proper citation: Conserved Domains Search (RRID:SCR_018729) Copy
https://github.com/yanzhanglab/Graph2GO
Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology.
Proper citation: Graph2GO (RRID:SCR_018726) Copy
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