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https://colororacle.org/

Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java.

Proper citation: Color Oracle (RRID:SCR_018400) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/omicsGAN

Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.

Proper citation: OmicsGAN (RRID:SCR_022976) Copy   

•   Source: SciCrunch Registry

https://www.sutter.com/manuals/P-2000_OpMan.pdf

Microprocessor controlled, CO2 laser based micropipette puller.Default configuration allows fabrication of micropipettes for intracellular recording, patch clamping, microinjection and microperfusion.Can store up to 100 separate programs, each consisting of up to 8 command lines. The five parameters set in each command line allow exquisite control of the micropipette taper geometry. Allows the use of wide range of glass diameters from 0.125 to 1.2 mm.

Proper citation: Sutter: P-2000 Laser Micropipette Puller (RRID:SCR_018640) Copy   

•   Source: SciCrunch Registry

https://www.vosviewer.com/

Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature.

Proper citation: VOSviewer (RRID:SCR_023516) Copy   

•   Source: SciCrunch Registry

http://www.pyomo.org/

Open source Python-based optimization modeling language with diverse set of optimization capabilities.

Proper citation: pyomo (RRID:SCR_024188) Copy   

•   Source: SciCrunch Registry

https://github.com/genome/bam-readcount

Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Proper citation: bam readcount (RRID:SCR_023653) Copy   

•   Source: SciCrunch Registry

https://www.transnetyx.com/colony?gad=1&gclid=CjwKCAjw8symBhAqEiwAaTA__GhOxQovqufxibmOSyRqtSo__-EMrnF9OGpdOAvAPgUOTE47h8TONBoCyMMQAvD_BwE

Software for mouse colony management. Streamlined software for simplified colony management.

Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy   

•   Source: SciCrunch Registry

http://statbio.github.io/Sargasso/

Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.

Proper citation: Sargasso (RRID:SCR_023489) Copy   

•   Source: SciCrunch Registry

http://samtools.github.io/htsjdk/

Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

Proper citation: HTSJDK (RRID:SCR_024036) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/Inspect/

Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.

Proper citation: InsPecT (RRID:SCR_024038) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg

Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases.

Proper citation: Brainreg (RRID:SCR_023858) Copy   

•   Source: SciCrunch Registry

https://github.com/klebgenomics/Kaptive

Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.

Proper citation: Kaptive (RRID:SCR_024046) Copy   

•   Source: SciCrunch Registry

https://www.jabref.org/

Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.

Proper citation: JabRef (RRID:SCR_024047) Copy   

•   Source: SciCrunch Registry

https://www.microsoft.com/en-my/microsoft-365/powerpoint

Presentation software developed by Microsoft Corporation. Part of Microsoft Office suite. Used for creating slideshows and delivering presentations.

Proper citation: Microsoft PowerPoint (RRID:SCR_023631) Copy   

•   Source: SciCrunch Registry

https://zonationteam.github.io/Zonation5/

Spatial prioritization software used to identify priority areas to support conservation planning, land use planning, ecological impact avoidance and other similar tasks.

Proper citation: Zonation 5 (RRID:SCR_023745) Copy   

•   Source: SciCrunch Registry

https://www.oracle.com/applications/crystalball/

Software spreadsheet based application for risk measurement and reporting, Monte Carlo simulation, time series forecasting, and optimization.Provides realistic and accessible way of modeling uncertainty, enabling you to measure and report on risk inherent in your key metrics.

Proper citation: Oracle Crystal Ball (RRID:SCR_023226) Copy   

•   Source: SciCrunch Registry

https://github.com/kblin/ncbi-acc-download

Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.

Proper citation: NCBI accession download script (RRID:SCR_024130) Copy   

•   Source: SciCrunch Registry

https://www.topazlabs.com/gigapixel-ai

Software to increase image resolution. Gigapixel AI’s neural networks are continuously trained on sample images to increase resolution of different subjects like portraits, wildlife, landscapes, architecture and image types like DSLR, web/compressed, CG.

Proper citation: Gigapixel AI (RRID:SCR_023684) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/de/de/home/digital-science/thermo-fisher-connect.html

Platform for connecting people, software, data, and equipment. Helps integrating software, instruments, and data across your lab’s existing ecosystem. Provides: workflows guide users through processes involving multiple systems;Centralized access to Thermo Fisher Scientific instrument service and expertise;Connectivity to monitor and maintain instruments and equipment;Granular data sharing controls to enhance collaboration;Secure environment.

Proper citation: ThermoFisher Connect Platform (RRID:SCR_023441) Copy   

•   Source: SciCrunch Registry

https://desmid.github.io/mview/

Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.

Proper citation: MView (RRID:SCR_024129) Copy   

•   Source: SciCrunch Registry