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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.
https://github.com/ParBLiSS/FastANI
Software tool for fast alignment free computation of whole genome Average Nucleotide Identity . Supports pairwise comparison of both complete and draft genome assemblies. to calcualte the average nucleotide identity (ANI) between your samples.
Proper citation: FastANI (RRID:SCR_021091) Copy
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
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
https://metacpan.org/dist/Bio-Chado-Schema
Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module.
Proper citation: Bio-Chado-Schema (RRID:SCR_024059) Copy
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
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Proper citation: pyomo (RRID:SCR_024188) Copy
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
https://metacpan.org/dist/AI-FANN
Software Perl wrapper for the Fast Artificial Neural Network library
Proper citation: AI-FANN (RRID:SCR_024060) Copy
https://metacpan.org/dist/Bio-Coordinate
Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
Proper citation: Bio-Coordinate (RRID:SCR_024063) Copy
Software for mouse colony management. Streamlined software for simplified colony management.
Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy
https://github.com/wkusmirek/mONiTor
Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process.
Proper citation: mONiTor (RRID:SCR_023921) Copy
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
Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.
Proper citation: Ginkgo CADx (RRID:SCR_024031) Copy
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
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
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
http://bibus-biblio.sourceforge.net/
Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records.
Proper citation: Bibus (RRID:SCR_023974) Copy
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
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
https://userbase.kde.org/KBibTeX
Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.
Proper citation: KBibTeX (RRID:SCR_024048) Copy
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