Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis.
Proper citation: Tissue Studio (RRID:SCR_023001) Copy
https://www.nitrc.org/projects/qcalign
Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas.
Proper citation: QCAlign (RRID:SCR_023088) Copy
http://colibread.inria.fr/software/mapsembler2/
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Proper citation: Mapsembler2 (RRID:SCR_024102) Copy
https://github.com/gerddie/maxflow
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Proper citation: MAXFLOW (RRID:SCR_024103) Copy
https://github.com/RabadanLab/arcasHLA
Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.
Proper citation: arcasHLA (RRID:SCR_022286) Copy
https://harvest.readthedocs.io/en/latest/content/parsnp.html
Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Proper citation: Parsnp (RRID:SCR_024153) Copy
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files.
Proper citation: PDB2PQR (RRID:SCR_024155) Copy
https://github.com/sib-swiss/pftools3
Software suite of tools to build and search generalized profiles.
Proper citation: PfTools (RRID:SCR_024158) Copy
https://jydu.github.io/physamp/
Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.
Proper citation: PhySamp (RRID:SCR_024159) Copy
Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.
Proper citation: BCALM 2 (RRID:SCR_023975) Copy
https://www.ncbi.nlm.nih.gov/books/NBK179288/
Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.
Proper citation: Entrez Direct (RRID:SCR_024136) Copy
https://doua.prabi.fr/software/njplot
Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Proper citation: NJplot (RRID:SCR_024137) Copy
https://www.syngene.com/software/genetools-automatic-image-analysis/
Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.
Proper citation: GeneTools (RRID:SCR_022505) Copy
https://github.com/PedroBarbosa/Prepare_SplicingPredictors
Software tool as set of scripts to prepare the input for several sequence-based RNA splicing methods from VCF files.
Proper citation: Prepare_SplicingPredictors (RRID:SCR_023316) Copy
https://github.com/wdecoster/NanoPlot
Software package as plotting tool for long read sequencing data and alignments.
Proper citation: NanoPlot (RRID:SCR_024128) Copy
https://pypi.org/project/OBITools/
Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.
Proper citation: OBITools (RRID:SCR_024141) Copy
https://freeimage.sourceforge.io/
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Proper citation: FreeImage (RRID:SCR_024022) Copy
https://www.orthanc-server.com/
Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.
Proper citation: Orthanc (RRID:SCR_024145) Copy
GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.
Proper citation: GDCM (RRID:SCR_024027) Copy
Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.
Proper citation: OpenIGTLink (RRID:SCR_024148) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within RRID that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
