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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/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
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
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
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
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
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