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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SpeedSeq Resource Report Resource Website 1+ mentions |
SpeedSeq (RRID:SCR_000469) | software resource | Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)). | standalone software |
is listed by: OMICtools has parent organization: University of Virginia; Virginia; USA |
Free, Available for download, Freely available | OMICS_04673 | SCR_000469 | 2026-08-01 12:01:18 | 7 | |||||||||
|
Health Level Seven International Resource Report Resource Website |
Health Level Seven International (RRID:SCR_000466) | HL7 | institution | ANSI-accredited standards developing organization providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7's 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare. HL7 provides standards for interoperability that improve care delivery, optimize workflow, reduce ambiguity and enhance knowledge transfer among all of their stakeholders, including healthcare providers, government agencies, the vendor community, fellow SDOs and patients. | health care, interoperability, health, health service, clinical, management | is parent organization of: Health Level Seven Reference Implementation Model Version 3 | nlx_157307, Wikidata: Q17054989, grid.434932.b | https://ror.org/029ga8k16 | SCR_000466 | 2026-08-01 12:01:18 | 0 | ||||||||
|
MATCHCLIP Resource Report Resource Website |
MATCHCLIP (RRID:SCR_000541) | MATCHCLIP | software resource | Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide. | breakpoint, deletion, duplication, exon sequencing, structural variation, next generation sequencing |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:23967014 | Free, Available for download, Freely available, | OMICS_02289 | SCR_000541 | matchclips2, MATCHCLIPS | 2026-08-01 12:01:15 | 0 | ||||||
|
Exonhit Therapeutics Resource Report Resource Website |
Exonhit Therapeutics (RRID:SCR_000493) | commercial organization | A drug and diagnostic discovery company. | drug, diagnostic, in vitro | is related to: PharmaCog | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158329 | SCR_000493 | Diaxonhit, Exonhit Therapeutics SA, ExonHit Therapeutics S.A. | 2026-08-01 12:01:19 | 0 | ||||||||
|
TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-08-01 12:01:19 | 0 | |||||||
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-08-01 12:01:20 | 14 | |||||
|
Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-08-01 12:01:20 | 22 | ||||||
|
SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-08-01 12:01:25 | 6 | ||||||
|
TNO-DECO Resource Report Resource Website |
TNO-DECO (RRID:SCR_000440) | software resource | Matlab code for preprocessing gas chromatography mass spectrometry data. | matlab, mass spectrometry | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02660 | SCR_000440 | 2026-08-01 12:01:13 | 0 | |||||||||
|
SNPiR Resource Report Resource Website 1+ mentions |
SNPiR (RRID:SCR_000557) | SNPiR | software resource | Software for reliable Identification of Genomic Variants Using RNA-seq Data. | genomic variant, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01362 | SCR_000557 | SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data | 2026-08-01 12:01:20 | 1 | |||||||
|
FPSAC Resource Report Resource Website 1+ mentions |
FPSAC (RRID:SCR_000555) | FPSAC | software resource | Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs. | genome, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:24068034 | biotools:fpsac, OMICS_00041 | https://bio.tools/fpsac | SCR_000555 | Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent, Fast Phylogenetic Scaffolding of Ancient Contigs, FPSAC: fast phylogenetic scaffolding of ancient contigs | 2026-08-01 12:01:15 | 1 | ||||||
|
ACCUSA2 Resource Report Resource Website |
ACCUSA2 (RRID:SCR_000558) | ACCUSA2 | software resource | Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores. | snv | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01360 | SCR_000558 | 2026-08-01 12:01:15 | 0 | ||||||||
|
RStudio Resource Report Resource Website 1000+ mentions |
RStudio (RRID:SCR_000432) | RStudio | software resource | Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux). | R, statistical, computing, environment |
is used by: PlotsOfData is listed by: Debian is listed by: SoftCite is related to: rSPRITE is related to: shinyCircoss is parent organization of: Shiny is required by: circlncRNAnet |
Restricted | SciRes_000113 | https://sources.debian.org/src/rstudio/, https://posit.co/download/rstudio-desktop/ | http://www.rstudio.com/ | SCR_000432 | 2026-08-01 12:01:13 | 1034 | ||||||
|
DySC Resource Report Resource Website |
DySC (RRID:SCR_000553) | DySC | software resource | Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy. | cluster, 16s rrna, read |
is listed by: OMICtools has parent organization: Google Code |
PMID:22730435 | Free, Available for download, Freely available, | OMICS_01443 | SCR_000553 | DySC: Software for Greedy Clustering of 16S rRNA Reads | 2026-08-01 12:01:24 | 0 | ||||||
|
drFAST Resource Report Resource Website 1+ mentions |
drFAST (RRID:SCR_000586) | drFAST | software resource | A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner. | di-base, solid color space, genome assemblies, memory-efficient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:21586516 | Free, Available for download, Freely available | biotools:drfast, OMICS_00661 | https://bio.tools/drfast | SCR_000586 | di-base read Fast Alignment Search Tool, drFAST: di-base read Fast Alignment Search Tool | 2026-08-01 12:01:21 | 1 | |||||
|
Genome BioInformatics Research Lab - gff2ps Resource Report Resource Website 1+ mentions |
Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format. | genome, sequence, visualization, parameters, bioinformatics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:11099262 DOI:10.1093/bioinformatics/16.8.743 |
Free, Available for download, Freely available | OMICS_17140, biotools:gff2ps, nif-0000-30611 | https://bio.tools/gff2ps, https://sources.debian.org/src/gff2ps/ | SCR_000462 | gff2ps | 2026-08-01 12:01:18 | 1 | ||||||
|
NGSmethPipe Resource Report Resource Website 1+ mentions |
NGSmethPipe (RRID:SCR_000583) | NGSmethPipe | software resource | A software tool which generates high-quality methylation maps. | computation, genomics, bioinformatics, methylation maps, visualization |
is listed by: OMICtools has parent organization: University of Granada; Granada; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00611 | SCR_000583 | NGSmethPipe - A tool to generate high-quality methylation maps | 2026-08-01 12:01:15 | 3 | |||||||
|
sybil - Efficient Constrained Based Modelling in R Resource Report Resource Website |
sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) | sybil | software resource | A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language. | unix/linux, windows, r |
is listed by: OMICtools is related to: SBML is related to: CRAN |
PMID:24224957 | Free, Available for download, Freely available | OMICS_06008 | http://www.cs.hhu.de/en/research-groups/bioinformatics/software/sybil.html | http://cran.r-project.org/web/packages/sybil/index.html | SCR_000457 | sybil: sybil - Efficient Constrained Based Modelling in R | 2026-08-01 12:01:13 | 0 | ||||
|
msbwt Resource Report Resource Website |
msbwt (RRID:SCR_000458) | software resource | A software package for creating, merging, and querying multi-string BWTs. | standalone software, python |
is listed by: OMICtools has parent organization: Google Code |
PMID:25172922 | Free, Available for download, Freely available | OMICS_05976 | https://code.google.com/p/msbwt/ | SCR_000458 | multi-string BWT | 2026-08-01 12:01:21 | 0 | ||||||
|
MAXCHELATOR Resource Report Resource Website 50+ mentions |
MAXCHELATOR (RRID:SCR_000459) | MAXC | software resource | A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration. | metal, concentration, chelator |
is related to: WEBMAXC STANDARD is related to: WEBMAXC EXTENDED has parent organization: Stanford University; Stanford; California |
PMID:8201981 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156862 | SCR_000459 | 2026-08-01 12:01:18 | 71 |
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