Tools   Select Another Resource Report Type

https://seaborn.pydata.org/

Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib.

Proper citation: seaborn (RRID:SCR_018132) Copy   

•   Source: SciCrunch Registry

https://lifesciencedb.jp/bp3d/

Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer.

Proper citation: Anatomography (RRID:SCR_018147) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

https://github.com/cramerlab/warp

Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising.

Proper citation: Warp (RRID:SCR_018071) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.agisoft.com

Stand alone software that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales. Successor of PhotoScan and is advanced image-based 3D modeling solution aimed at creating professional quality 3D content from still images.

Proper citation: Agisoft Metashape (RRID:SCR_018119) Copy   

•   Source: SciCrunch Registry

http://raptorx.uchicago.edu/

Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.

Proper citation: RaptorX (RRID:SCR_018118) Copy   

•   Source: SciCrunch Registry

https://view.qiime2.org/

Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided.

Proper citation: QIIME 2 View (RRID:SCR_018074) Copy   

•   Source: SciCrunch Registry

http://flowpy.wikidot.com/

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   

•   Source: SciCrunch Registry

http://www.premierbiosoft.com/protein_quantification_software/index.html

Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS.

Proper citation: PremierBiosoft Proteo IQ Software (RRID:SCR_018072) Copy   

•   Source: SciCrunch Registry

http://circadb.hogeneschlab.org/

Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.

Proper citation: CircaDB (RRID:SCR_018078) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.milesculabs.org/QuB.html

Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: QuB (RRID:SCR_018076) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/cowplot/index.html

Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images.

Proper citation: cowplot (RRID:SCR_018081) Copy   

•   Source: SciCrunch Registry

https://vivli.org/

Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.

Proper citation: Vivli (RRID:SCR_018080) Copy   

•   Source: SciCrunch Registry

http://ultrascan.aucsolutions.com/

Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.

Proper citation: UltraScan (RRID:SCR_018126) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://clipseq.usegalaxy.eu/

Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP.

Proper citation: CLIP-Explorer (RRID:SCR_018128) Copy   

•   Source: SciCrunch Registry

http://www.imperial.ac.uk/research/animallectins

Resource presents information about animal lectins involved in various sugar recognition processes.

Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy   

•   Source: SciCrunch Registry