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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.
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Proper citation: python-biom-format (RRID:SCR_024193) 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
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Proper citation: pyomo (RRID:SCR_024188) 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 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
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
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
Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.
Proper citation: Lucy (RRID:SCR_024099) Copy
Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux.
Proper citation: Aeskulap (RRID:SCR_023960) Copy
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
http://rambok.sourceforge.net/
Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.
Proper citation: rambo-k (RRID:SCR_024198) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-TCoffee
Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.
Proper citation: Bio-Tools-Run-Alignment-TCoffee (RRID:SCR_024070) Copy
https://github.com/miRTop/mirtop
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Proper citation: mirtop (RRID:SCR_024116) Copy
https://sourceforge.net/projects/mpsqed/
Software tool for the design of multiplex pyrosequencing assays.
Proper citation: mPSQed (RRID:SCR_024118) Copy
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