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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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bam readcount Resource Report Resource Website 10+ mentions |
bam readcount (RRID:SCR_023653) | software resource, software application | 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. | BAM file, CRAM file, sequencing data, nucleotide positions, | NCI R50CA211782; NCI P01CA101937; NCI K22CA188163; NCI 1U01CA209936; NCI U24CA237719; Edward P. Evans Foundation ; NHGRI R00 HG007940 |
PMID:34341766 | Free, Available for download, Freely available | SCR_023653 | bam-readcount | 2026-08-12 10:52:50 | 38 | ||||||||
|
AI-FANN Resource Report Resource Website |
AI-FANN (RRID:SCR_024060) | software resource, software application | Software Perl wrapper for the Fast Artificial Neural Network library | Perl wrapper, Fast Artificial Neural Network library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libai-fann-perl/ | SCR_024060 | AI-FANN - Perl wrapper for the Fast Artificial Neural Network library, libai-fann-perl | 2026-08-12 10:53:02 | 0 | ||||||||
|
Bio-Coordinate Resource Report Resource Website |
Bio-Coordinate (RRID:SCR_024063) | software resource, software application | Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. | biological coordinate systems, | is listed by: Debian | https://sources.debian.org/src/libbio-coordinate-perl/ | SCR_024063 | Bio-Coordinate - Modules for working with biological coordinates, libbio-coordinate-perl | 2026-08-12 10:53:09 | 0 | |||||||||
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Transnetyx Colony Management Resource Report Resource Website 1+ mentions |
Transnetyx Colony Management (RRID:SCR_023922) | software resource, software application | Software for mouse colony management. Streamlined software for simplified colony management. | Transnetyx, Inc., mouse colony management, simplified colony management, colony management, | Restricted | SCR_023922 | 2026-08-12 10:52:54 | 1 | |||||||||||
|
mONiTor Resource Report Resource Website |
mONiTor (RRID:SCR_023921) | software resource, software application | 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. | Oxford Nanopore Technology, Oxford Nanopore Technology sequencing, monitoring nanopore sequencing process, monitoring process, nanopore sequencing process, nanopore sequencing, | Free, Available for download, Freely available | SCR_023921 | 2026-08-12 10:53:00 | 0 | |||||||||||
|
Sargasso Resource Report Resource Website 1+ mentions |
Sargasso (RRID:SCR_023489) | software resource, software application | Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin. | disambiguate mixed species RNA-seq reads, mixed species RNA-seq reads, mixed species, RNA-seq reads | Free, Available for download, Freely available | https://zenodo.org/record/260123#.ZEG6ynbMK3B | SCR_023489 | 2026-08-12 10:53:02 | 1 | ||||||||||
|
Ginkgo CADx Resource Report Resource Website |
Ginkgo CADx (RRID:SCR_024031) | software resource, software application | Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files. | Digital Imaging and Communication In Medicine, DICOM viewer, dicomizer, convert files, png, jpeg, bmp, pdf, tiff, convert to DICOM files, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/ginkgocadx/, https://github.com/gerddie/ginkgocadx | SCR_024031 | ginkgocadx | 2026-08-12 10:53:08 | 0 | ||||||||
|
HTSJDK Resource Report Resource Website 1+ mentions |
HTSJDK (RRID:SCR_024036) | software resource, software application | 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. | accessing common file formats, SAM, VCF, manipulating HTS data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htsjdk/, https://github.com/samtools/htsjdk | SCR_024036 | htsjdk | 2026-08-12 10:52:56 | 4 | ||||||||
|
InsPecT Resource Report Resource Website 1+ mentions |
InsPecT (RRID:SCR_024038) | software resource, software application | 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. | addresses algorithmic problems, identify modified proteins, post-translational modification identification, | is listed by: Debian | PMID:16013882 | Free, Available for download, Freely available, | OMICS_02397 | https://sources.debian.org/src/inspect/ | SCR_024038 | Inspect, inspect | 2026-08-12 10:53:02 | 1 | ||||||
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Brainreg Resource Report Resource Website 1+ mentions |
Brainreg (RRID:SCR_023858) | software resource, software application | 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. | Allen Mouse Brain Reference Atlas, Allen Human Brain Atlas, Allen Reference Atlas, template brain registration, sample image, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023858 | 2026-08-12 10:52:54 | 6 | ||||||||||
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Bibus Resource Report Resource Website |
Bibus (RRID:SCR_023974) | software resource, software application | Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records. | Bibliographic and reference management, bibliographic records, search bibliographic records, edit bibliographic records, sort bibliographic records, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bibus/ | SCR_023974 | bibus | 2026-08-12 10:53:07 | 0 | ||||||||
|
Kaptive Resource Report Resource Website 10+ mentions |
Kaptive (RRID:SCR_024046) | software resource, software application | Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies. | report information, surface polysaccharide loci, genome assemblies, | is listed by: Debian | PMID:28348840 | Free, Available for download, Freely available, | OMICS_27932 | https://sources.debian.org/src/kaptive/ | SCR_024046 | kaptive | 2026-08-12 10:53:08 | 18 | ||||||
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JabRef Resource Report Resource Website 1+ mentions |
JabRef (RRID:SCR_024047) | software resource, software application | Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research. | citation and reference, management tool, collect and organize sources, find the paper, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/jabref-plugin-oo/, https://github.com/JabRef/jabref | SCR_024047 | jabref, JabRef Bibliography Management | 2026-08-12 10:53:02 | 4 | ||||||||
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KBibTeX Resource Report Resource Website |
KBibTeX (RRID:SCR_024048) | software resource, software application | 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. | bibliography editor for KDE, bibliography editor, BibTeX editor for KDE, | is listed by: Debian | Restricted | https://sources.debian.org/src/kbibtex/ | SCR_024048 | kbibtex | 2026-08-12 10:52:56 | 0 | ||||||||
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Microsoft PowerPoint Resource Report Resource Website 100+ mentions |
Microsoft PowerPoint (RRID:SCR_023631) | software resource, software application | Presentation software developed by Microsoft Corporation. Part of Microsoft Office suite. Used for creating slideshows and delivering presentations. | Microsoft Corporation, Microsoft Office, creating slideshows, delivering presentations, presentation software, | Restricted | SCR_023631 | 2026-08-12 10:52:57 | 115 | |||||||||||
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Zonation 5 Resource Report Resource Website 1+ mentions |
Zonation 5 (RRID:SCR_023745) | software resource, software application | Spatial prioritization software used to identify priority areas to support conservation planning, land use planning, ecological impact avoidance and other similar tasks. | Spatial prioritization, identify priority areas, support conservation planning, land use planning, ecological impact avoidance, | Free, Available for download, Freely available | https://github.com/zonationteam/Zonation5 | SCR_023745 | Zonation 5 v1.0 | 2026-08-12 10:53:05 | 1 | |||||||||
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Oracle Crystal Ball Resource Report Resource Website 1+ mentions |
Oracle Crystal Ball (RRID:SCR_023226) | software resource, software application | 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. | Spreadsheet based application, risk measurement and reporting, Monte Carlo simulation, time series forecasting, optimization | Restricted | SCR_023226 | 2026-08-12 10:52:44 | 4 | |||||||||||
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NCBI accession download script Resource Report Resource Website 1000+ mentions |
NCBI accession download script (RRID:SCR_024130) | software resource, software application | 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. | download sequences, GenBank/RefSeq, accession through NCBI ENTREZ API, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/ncbi-acc-download/ | SCR_024130 | ncbi-acc-download | 2026-08-12 10:52:59 | 1179 | ||||||||
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Lucy Resource Report Resource Website |
Lucy (RRID:SCR_024099) | software resource, software application | Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. | clean sequence data from automated DNA sequencers, Sanger sequencing, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_14823 | https://sources.debian.org/src/lucy/ | SCR_024099 | lucy, Lucy DNA sequence quality and vector trimming tool | 2026-08-12 10:53:09 | 0 | |||||||
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Aeskulap Resource Report Resource Website |
Aeskulap (RRID:SCR_023960) | software resource, software application | 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. | medical image viewer, Digital Imaging and Communications in Medicine, DICOM, DICOM viewer, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/aeskulap/ | SCR_023960 | Aeskulap - DICOM Viewer, aeskulap | 2026-08-12 10:53:00 | 0 |
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