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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data analysis software, data processing software, sequence analysis software, software application, software resource | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | SciCrunch Registry | 2026-09-26 02:12:54 | 0 | |||||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | SciCrunch Registry | 2026-09-26 02:12:54 | 0 | |||||||
|
Howard University; Washington D.C. Resource Report Resource Website |
Howard University; Washington D.C. (RRID:SCR_001084) | HU | university | A federally chartered, private, coeducational, nonsectarian, historically black university in Washington, D.C. Howard University has graduate schools in many fields, including business, nursing, engineering, and medicine. | undergraduate, graduate, master's, doctoral, phD, institution, university, nonsectarian |
is related to: Clinical and Translational Science Awards Consortium is parent organization of: Howard Flow Cytometry Core is parent organization of: Howard Imaging Core Facility: Molecular Imaging Laboratory is parent organization of: Howard Biobehavioral Core Laboratory is parent organization of: Howard Biostatistics Core is parent organization of: Howard University Center for Computational Biology and Bioinformatics Core Facility is parent organization of: Howard Molecular Genetics Core is parent organization of: Howard Nanoscale Science and Engineering Facility is parent organization of: Howard RCMI Proteomics Facility |
nlx_152178 | SCR_001084 | SciCrunch Registry | Howard, Howard University, Howard U | 2026-09-26 02:12:54 | 0 | ||||||||
|
University of Florida College of Medicine Neuroscience Resource Report Resource Website |
University of Florida College of Medicine Neuroscience (RRID:SCR_001081) | data or information resource, department portal, organization portal, portal | A department at the University of Florida's College of Medicine that offers programs of study on neural function and how it changes with injury and disease. The institution's research ranges from fundamental discovery to clinical application. These neuroscience programs are offered at the undergraduate, graduate, postdoctoral and resident level. | neuroscience, neural function, undergraduate, graduate, postdoctoral, resident, clinical, injury, disease | nif-0000-02172 | SCR_001081 | SciCrunch Registry | UFL | 2026-09-26 02:12:54 | 0 | ||||||||||
|
Simpleaffy Resource Report Resource Website 50+ mentions |
Simpleaffy (RRID:SCR_001302) | Simpleaffy | data analysis software, data processing software, software application, software resource | Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures. | affymetrix, annotation, data import, differential expression, microarray, one channel, preprocessing, quality control, report writing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16076888 | GNU General Public License, v2 or newer | OMICS_02034 | SCR_001302 | SciCrunch Registry | Simpleaffy - Very simple high level analysis of Affymetrix data | 2026-09-26 02:12:58 | 85 | ||||||
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BSSim Resource Report Resource Website 1+ mentions |
BSSim (RRID:SCR_001212) | BSSim | software resource | Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD. | bisulfite sequencing, simulator, next-generation sequencing, python, dna methylation, snp, read quality | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02130 | SCR_001212 | SciCrunch Registry | BSSim: Bisulfite sequencing simulator for next-generation sequencing | 2026-09-26 02:12:56 | 1 | |||||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NSF CLS20163A; Sloan Research Fellowship |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | SciCrunch Registry | 2026-09-26 02:12:56 | 0 | ||||||
|
QualiMap Resource Report Resource Website 10+ mentions |
QualiMap (RRID:SCR_001209) | QualiMap | software resource | Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis. | next-generation sequencing, alignment, linux, macos, windows, quality control, sam, bam, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Economy and Competitiveness BIO2009-10799; EU funded program ERA-NET PathoGenoMics BIO2008-05266-E |
PMID:22914218 DOI:10.1093/bioinformatics/bts503 |
Free, Available for download, Freely available | OMICS_02133, biotools:qualimap | https://bio.tools/qualimap | https://sources.debian.org/src/qualimap/ | SCR_001209 | SciCrunch Registry | QualiMap - Evaluating next generation sequencing alignment data | 2026-09-26 02:12:56 | 48 | |||
|
Omixon Target Data Analysis Resource Report Resource Website |
Omixon Target Data Analysis (RRID:SCR_001207) | Omixon Target | commercial organization, data analysis software, data processing software, software application, software resource, software toolkit | Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets. | next-generation sequencing, gene target, windows, linux, mac, gene, diagnostic |
is listed by: OMICtools is parent organization of: Omixon Target HLA Typing |
License required | OMICS_02141 | SCR_001207 | SciCrunch Registry | 2026-09-26 02:12:56 | 0 | ||||||||
|
North Dakota State University; North Dakota; USA Resource Report Resource Website 1+ mentions |
North Dakota State University; North Dakota; USA (RRID:SCR_001110) | NDSU | university | Public research university in North Dakota, USA. It is a land-grant university that focuses on agriculture and the applied sciences. In addition, it offers undergraduate and graduate degrees in a wide variety of areas including engineering, science and mathematics, health professions, business, and agriculture and food systems studies. | public, research, land grant, agriculture, applied sciences, food systems, health profession |
is parent organization of: NDSU Center for Protease Research is parent organization of: North Dakota State University Labs and Facilities is parent organization of: North Dakota State University School of Pharmacy; North Dakota; USA |
Wikidata:Q2000624, grid.261055.5, nlx_71768, ISNI:0000 0001 2293 4611, Crossref funder ID:100007518 | https://ror.org/05h1bnb22 | SCR_001110 | SciCrunch Registry | North Dakota State University | 2026-09-26 02:12:55 | 1 | |||||||
|
Genome Trax Resource Report Resource Website 1+ mentions |
Genome Trax (RRID:SCR_001234) | Genome Trax | service resource | Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia. | next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, database, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: BIOBASE Corporation |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02109, biotools:genome_trax | https://bio.tools/genome_trax | SCR_001234 | SciCrunch Registry | Genome Trax for Next Generation Sequencing | 2026-09-26 02:12:56 | 2 | ||||||
|
Speech Perception Resource Report Resource Website |
Speech Perception (RRID:SCR_001114) | data or information resource, portal, topical portal | An entry of the Cognitive Atlas which defines the term speech perception. | cognitive science, language, processing language | is related to: Cognitive Atlas | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_145380 | SCR_001114 | SciCrunch Registry | 2026-09-26 02:12:55 | 0 | |||||||||
|
PHACCS Resource Report Resource Website 1+ mentions |
PHACCS (RRID:SCR_001232) | software resource | Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15743531 | Free, Available for download, Freely available | OMICS_03529 | SCR_001232 | SciCrunch Registry | 2026-09-26 02:12:56 | 1 | ||||||||
|
QUAST Resource Report Resource Website 1000+ mentions |
QUAST (RRID:SCR_001228) | QUAST | software resource | Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots. | genome assembly, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia has parent organization: SourceForge |
PMID:23422339 | biotools:quast, OMICS_02115 | https://bio.tools/quast, https://sources.debian.org/src/quast/ | SCR_001228 | SciCrunch Registry | QUAST: Quality Assessment Tool for Genome Assemblies | 2026-09-26 02:12:56 | 3293 | ||||||
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R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | SciCrunch Registry | 2026-09-26 02:12:55 | 4 | ||||||||
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Academy Biomedical Company Resource Report Resource Website |
Academy Biomedical Company (RRID:SCR_001108) | commercial organization | Commercial antibody supply company that focuses on providing antibodies for research in cardiovascular and atherosclerosis. | antibody, cardiovascular, athersclerosis, antibody supplier | nlx_152249 | SCR_001108 | SciCrunch Registry | Academy Bio-Medical Company, Academy Biomedical Company Inc. | 2026-09-26 02:12:55 | 0 | ||||||||||
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TileQC Resource Report Resource Website |
TileQC (RRID:SCR_001229) | TileQC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh). | next-generation sequencing, quality control, solexa, r, tile, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Oregon State University; Oregon; USA |
PMID:18507856 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tileqc, OMICS_02114 | https://bio.tools/tileqc | SCR_001229 | SciCrunch Registry | TileQC: A tile based approached to quality control | 2026-09-26 02:12:56 | 0 | |||||
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ChanTest Resource Report Resource Website 10+ mentions |
ChanTest (RRID:SCR_001220) | CT | commercial organization | An ion channel focused Contract Research Organization (CRO) that does safety testing and screening for global pharma and biotech companies. ChanTest has developed a complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers. Services range from early functional screens for profiling drug candidates or ranking within profiles during the drug-discovery process to a complete set of in vitro GLP service products for cardiac risk assessment. ChanTest works in partnership with customers to speed the drug-development process, save time and money, and ultimately to help make better, safer drugs. | ion channel, safety testing, screening, drug, drug development | nlx_152331 | http://chantest.com | SCR_001220 | SciCrunch Registry | ChanTest.com | 2026-09-26 02:12:56 | 12 | ||||||||
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BreakFusion Resource Report Resource Website 1+ mentions |
BreakFusion (RRID:SCR_001102) | BreakFusion | software resource | Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data. | computational pipeline, gene fusions, rna, sequence, data, perl, c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:22563071 DOI:10.1093/bioinformatics/bts272 |
Free, Available for download, Freely available | OMICS_01342 | SCR_001102 | SciCrunch Registry | 2026-09-26 02:12:55 | 3 | |||||||
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Body System Terms from ICD11 Resource Report Resource Website |
Body System Terms from ICD11 (RRID:SCR_001252) | ICD11-BODYSYSTEM | controlled vocabulary, data or information resource, ontology | Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision | owl | is listed by: BioPortal | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157339 | SCR_001252 | SciCrunch Registry | 2026-09-26 02:12:57 | 0 |
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