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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GEOMAGIC Studio Resource Report Resource Website 1+ mentions |
GEOMAGIC Studio (RRID:SCR_016978) | GEOMAGIC Studio 12 | data processing software, software application, software resource | Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis. | 3D, scan, convert, data, surface, polygon, native, CAD, model | Free, Available for download, Freely available | https://de.3dsystems.com/press-releases/geomagic/studio-12-offers-fastest-way-to-convert-3d-scans-of-phy | SCR_016978 | SciCrunch Registry | 2026-10-24 12:50:01 | 1 | |||||||||
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Albacore Resource Report Resource Website 100+ mentions |
Albacore (RRID:SCR_015897) | data processing software, software application, software resource | Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data. | sequence, dna, raw data, event detection, single-read, nanopore, basecaller, basecaller software, dockerfile | Free, Available for download | SCR_015897 | SciCrunch Registry | 2026-10-24 12:50:01 | 437 | |||||||||||
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Natural Stress Relief Resource Report Resource Website |
Natural Stress Relief (RRID:SCR_015898) | NSR | data or information resource, organization portal, portal | Organization that provides instructions for and research on the Natural Stress Relief (NSR) meditation method. | stress, relief, natural, organization, non-profit, research, mediation | SCR_015898 | SciCrunch Registry | 2026-10-24 12:50:00 | 0 | |||||||||||
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QDSpy Resource Report Resource Website 1+ mentions |
QDSpy (RRID:SCR_016985) | QDSpy | data processing software, software application, software resource | Software Python tool for scripting and presenting stimuli for visual neuroscience. | scripting, presenting, stimuli, visual, neuroscience | Free, Available for download, Freely available | http://qdspy.eulerlab.de/ | SCR_016985 | SciCrunch Registry | Quality Data System python software | 2026-10-24 12:50:01 | 7 | ||||||||
|
STRUCTURE Resource Report Resource Website 1000+ mentions |
STRUCTURE (RRID:SCR_017637) | software resource, software toolkit | Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms. | Multi locus genotype data, investigate population structure, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: STRAT has parent organization: Stanford University; Stanford; California works with: Structure Harvester |
PMID:21564903 PMID:18784791 PMID:12930761 PMID:10835412 |
Free, Available for download, Freely available | SCR_021634, nlx_154662, SCR_002151, biotools:structure | https://bio.tools/structure, http://pritch.bsd.uchicago.edu/structure.html, | SCR_017637 | SciCrunch Registry | structure, Structure | 2026-10-24 12:50:04 | 4177 | ||||||
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | atlas, data or information resource, reference atlas | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | SciCrunch Registry | 2026-10-24 12:50:03 | 5 | |||||||||
|
GNU sed Resource Report Resource Website 1+ mentions |
GNU sed (RRID:SCR_018215) | data processing software, software application, software resource | Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file. | Text editor, filter text, modify text, pattern matching extraction, matching occurrences replaced, substitute occurrence, text processing | Free Software Foundation | Free, Available for download, Freely available | SCR_018215 | SciCrunch Registry | GNU stream editor | 2026-10-24 12:50:04 | 2 | |||||||||
|
Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | data processing software, software application, software resource | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
A*STAR ; Singapore ; Croatian Academy of Sciences and Arts ; Croatian Science Foundation |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | SciCrunch Registry | 2026-10-24 12:50:03 | 177 | ||||||
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seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software application, software resource, software toolkit, standalone software | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | SciCrunch Registry | 2026-10-24 12:50:06 | 1 | ||||||||
|
GNU Grep Resource Report Resource Website 1+ mentions |
GNU Grep (RRID:SCR_018212) | data processing software, software application, software resource | Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options. | Print line, match pattern, input file, match search, pattern, plain text data, data set, match regular expression | Free, Freely available | SCR_018212 | SciCrunch Registry | GNU Grep 3.4, Grep | 2026-10-24 12:50:05 | 5 | ||||||||||
|
TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, software resource, standalone software | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | SciCrunch Registry | , Find Coding Regions Within Transcripts | 2026-10-24 12:50:04 | 1572 | |||||||
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LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | data processing software, software application, software resource | Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies. | Chromosome, scale, scaffolding, de novo, genome, assembly, chromatin, Hi-C, data, clustering, contig | National Science Foundation ; NHGRI HG006283; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | SciCrunch Registry | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-10-24 12:50:03 | 70 | ||||||||
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GNU Tar Resource Report Resource Website 1+ mentions |
GNU Tar (RRID:SCR_018216) | data processing software, software application, software resource | Software tool to create tar archives, as well as various other kinds of manipulation. Used to extract files, to store additional files, or to update or list files which were already stored. Can direct its output to available devices, files, or other programs, can access remote devices or files. | Archive, extract file, store file, update file, list file, access device, access file | Free Software Foundation | Free, Available for download, Freely available | SCR_018216 | SciCrunch Registry | GNU Tape archiver | 2026-10-24 12:50:03 | 3 | |||||||||
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Mnemiopsis Genome Project Portal Resource Report Resource Website |
Mnemiopsis Genome Project Portal (RRID:SCR_018293) | MGP Portal | data or information resource, portal, project portal | Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis. | Genomic, data, metazoan development, Mnemiopsis leidyi, Ctenophore, moel organisms, genomic data analysis |
is related to: University of Michigan; Ann Arbor; USA is related to: Brown University; Rhode Island; USA is related to: University of Florida; Florida; USA |
Free, Freely available | SCR_018293 | SciCrunch Registry | 2026-10-24 12:50:05 | 0 | |||||||||
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Twins Research Australia Resource Report Resource Website 1+ mentions |
Twins Research Australia (RRID:SCR_017485) | data or information resource, portal | Portal for Twins Research Australia. Brings twins and researchers together for vital health research in twins. | Twin, research, Australia, data | has parent organization: University of Melbourne; Victoria; Australia | National Health and Medical Research Council | Free, Freely available | SCR_017485 | SciCrunch Registry | Australian Twin Registry | 2026-10-24 12:50:02 | 4 | ||||||||
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GNU Awk Resource Report Resource Website 1+ mentions |
GNU Awk (RRID:SCR_018211) | GAWK | data processing software, software application, software resource | Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors. | Select record in file, perform operation of file, data reformatiing | Free, Freely available | SCR_018211 | SciCrunch Registry | 2026-10-24 12:50:03 | 7 | ||||||||||
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KOMP2 Resource Report Resource Website 1+ mentions |
KOMP2 (RRID:SCR_017528) | data or information resource, portal, project portal | Knockout Mouse Phenotyping Project, JAX information about their contributions to KOMP2 project. Project to generate and phenotype single gene KO mouse strains from KOMP ES cell lines. Strains are phenotyped using protocols in pipeline designed by International Mouse Phenotyping Consortium. There are three NIH-funded phenotyping centers in United States: JAX, BaSH Consortium (Baylor College of Medicine, the Wellcome Trust Sanger Institute and MRC Harwell), and the DTCC Consortium (University of California at Davis, the Toronto Center for Phenogenomics, Children’s Hospital Oakland Research Institute (CHORI) and Charles River ). | Generate, phenotype, single, gene, KO mouse, strain, KOMP ES cell line, IMPC, JAX |
is related to: International Mouse Phenotyping Consortium (IMPC) is related to: Knockout Mouse Project is related to: Knockout Mouse Project |
NIH | Free, Freely available | SCR_017528 | SciCrunch Registry | Knockout Mouse Phenotyping Project | 2026-10-24 12:50:02 | 2 | ||||||||
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Rhesus Macaque Brain Atlases Resource Report Resource Website |
Rhesus Macaque Brain Atlases (RRID:SCR_017533) | atlas, data or information resource, data set | Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque. | Collection, atlas, data, scan, functional, structural, imaging, rhesus macaque | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | http://brainmap.wisc.edu/monkey.html | SCR_017533 | SciCrunch Registry | 2026-10-24 12:50:02 | 0 | |||||||||
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Corneal Diseases Classification Resource Report Resource Website |
Corneal Diseases Classification (RRID:SCR_017416) | data processing software, image analysis software, software application, software resource | Software based on deep learning model for auto detect corneal diseases. Sample may contain multiple categories. After learning thousands of corneal images, you can make automatic judgments on subtypes of cornea. | Deep, learning, model, auto detect, corneal, disease, classification | Free, Available for download, Freely available | SCR_017416 | SciCrunch Registry | 2026-10-24 12:50:02 | 0 | |||||||||||
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Purge_haplotigs Resource Report Resource Website 10+ mentions |
Purge_haplotigs (RRID:SCR_017616) | data processing software, software application, software resource | Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies. | Reassigning, primary, contig, label, haplotig, third, generation, sequencing, assembly, allelic, curation, genome, alignment | PMID:30497373 | Free, Available for download, Freely available | SCR_017616 | SciCrunch Registry | 2026-10-24 12:50:02 | 14 |
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