Searching the RRID Resource Information Network

Our searching services are busy right now. Please try again later

  • Register
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X

Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

No
Yes

Preparing word cloud

×

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.

Search

Type in a keyword to search

Filter by records added date
See new records

Options


Current Facets and Filters

  • Related Resources:bio.tools (facet)

Facets


Recent searches

Snippet view Table view
Click the to add this resource to a Collection

1,660 Results - per page

Show More Columns | Download Top 1000 Results

Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
limmaGUI
 
Resource Report
Resource Website
10+ mentions
limmaGUI (RRID:SCR_001306) limmaGUI software resource Software package for a Graphical User Interface for the limma Microarray package. differential expression, gui, microarray, multiple comparison, preprocessing, quality control, two channel, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:15297296 Free, Available for download, Freely available OMICS_02027, biotools:limmagui https://bio.tools/limmagui SCR_001306 limmaGUI - GUI for limma package 2026-09-19 12:49:38 14
ffpe
 
Resource Report
Resource Website
500+ mentions
ffpe (RRID:SCR_001307) ffpe software resource Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). formalin-fixed, paraffin-embedded, gene expression, microarray, quality control, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
Free, Available for download, Freely available OMICS_02026, biotools:ffpe https://bio.tools/ffpe SCR_001307 ffpe - Quality assessment and control for FFPE microarray expression data 2026-09-19 12:49:38 524
NetNGlyc
 
Resource Report
Resource Website
1000+ mentions
NetNGlyc (RRID:SCR_001570) NetNGlyc analysis service resource, data analysis service, production service resource, service resource, software application, software resource Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. predict, n-glycosylation site, human, protein, neural network, sequence, asn-xaa-ser/thr sequon, glycoprotein, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: CBS Prediction Servers
Free, Freely available nlx_153863, biotools:netnglyc https://bio.tools/netnglyc SCR_001570 NetNGlyc Server 2026-09-19 12:49:43 1828
YinOYang
 
Resource Report
Resource Website
100+ mentions
YinOYang (RRID:SCR_001605) YinOYang analysis service resource, data analysis service, production service resource, service resource, software application, software resource Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. neural network, prediction, o-beta-glcnac attachment site, protein sequence, protein, sequence, glycosylation site, proteome, post-translational modification, protein function, glycoprotein, bio.tools uses: NetPhos
is listed by: bio.tools
is listed by: Debian
has parent organization: CBS Prediction Servers
Danish National Research Foundation PMID:11928486 Free, Freely available nlx_153865, biotools:yinoyang https://bio.tools/yinoyang SCR_001605 2026-09-19 12:49:43 118
Clustal Omega
 
Resource Report
Resource Website
10000+ mentions
Clustal Omega (RRID:SCR_001591) Clustal Omega, Clustalo alignment software, data processing software, image analysis software, service resource, software application, software resource Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF. multiple, sequence, alignment, DNA, RNA, protein, generate, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Clustal W2
is related to: Clustal W2
is related to: Clustal 2
has parent organization: European Bioinformatics Institute
has parent organization: University College Dublin; Dublin; Ireland
Science Foundation Ireland PMID:21988835
PMID:20439314
DOI:10.1038/msb.2011.75
Free, Available for download, Freely available OMICS_00972, SCR_016062, biotools:clustalo, nlx_153836 https://sources.debian.org/src/clustalo/, http://www.clustal.org/omega/, http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-multialign, https://bio.tools/clustalo, https://sources.debian.org/src/clustalo/ SCR_001591 2026-09-19 12:49:44 10580
asSeq
 
Resource Report
Resource Website
1+ mentions
asSeq (RRID:SCR_001625) asSeq data analysis software, data processing software, software application, software resource, source code Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Bioconductor
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
PMID:21838806 Free, Available for download, Freely available OMICS_01948, nlx_153893, biotools:asseq https://bio.tools/asseq SCR_001625 2026-09-19 12:49:44 6
PyLOH
 
Resource Report
Resource Website
1+ mentions
PyLOH (RRID:SCR_001511) software resource Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. standalone software, python, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:24695406 Free, Available for download, Freely available OMICS_03559, biotools:pyloh https://bio.tools/pyloh SCR_001511 2026-09-19 12:49:42 6
MatrixDB
 
Resource Report
Resource Website
50+ mentions
MatrixDB (RRID:SCR_001727) MatrixDB data or information resource, database, production service resource, service resource Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: IMEx - The International Molecular Exchange Consortium
is related to: Gene Ontology
is related to: PSI-MI
is related to: HPRD - Human Protein Reference Database
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: IMEx - The International Molecular Exchange Consortium
is related to: PSICQUIC Registry
is related to: IntAct
has parent organization: Claude Bernard University Lyon 1; Lyon; France
European Union contract FP7-HEALTH-2007-223411 PMID:20852260
PMID:19147664
THIS RESOURCE IS NO LONGER IN SERVICE biotools:matrixdb, r3d100010672, nif-0000-10226 https://bio.tools/matrixdb, https://doi.org/10.17616/R3M03H http://matrixdb.ibcp.fr/ SCR_001727 MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database 2026-09-19 12:49:46 95
Biocatalogue - The Life Science Web Services Registry
 
Resource Report
Resource Website
1+ mentions
Biocatalogue - The Life Science Web Services Registry (RRID:SCR_001679) BioCatalogue data access protocol, data or information resource, database, software resource, web service Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services. biological, web, life science, programmatic access, bioinformatics, registry, annotation, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: MetaLocGramN
is related to: myExperiment
is related to: bioDBcore
has parent organization: European Bioinformatics Institute
has parent organization: University of Manchester; Manchester; United Kingdom
European Union LHSG-CT-2004-512092;
EMBO ASTF 338.00-2009
PMID:20484378 THIS RESOURCE IS NO LONGER IN SERVICE biotools:biocatalogue, nif-0000-10167 https://bio.tools/biocatalogue SCR_001679 Biocatalog 2026-09-19 12:49:45 7
TANGO
 
Resource Report
Resource Website
100+ mentions
TANGO (RRID:SCR_001770) TANGO software resource A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions. polypeptide chain, polypeptide, peptide, protein, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Center for Genomic Regulation; Barcelona; Spain
PMID:15361882 Free, Freely available biotools:tango, OMICS_03859 https://bio.tools/tango SCR_001770 2026-09-19 12:49:46 136
Cuffdiff
 
Resource Report
Resource Website
1000+ mentions
Cuffdiff (RRID:SCR_001647) Cuffdiff software resource Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. differential expression, rna-seq, transcript, splicing, promoter, coding sequence, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Cufflinks
has parent organization: University of Maryland; Maryland; USA
PMID:23222703 Free, Available for download, Freely available biotools:cuffdiff, OMICS_01969 https://bio.tools/cuffdiff SCR_001647 Cuffdiff 2 2026-09-19 12:49:44 3925
MetaBase
 
Resource Report
Resource Website
50+ mentions
MetaBase (RRID:SCR_001762) MB data or information resource, database, narrative resource, wiki User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities. biological, mediawiki, biology, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Genome Research Foundation
MKE - Ministry of Knowledge Economy PMID:22139927 Free, Freely available biotools:metabase, nif-0000-10293 https://bio.tools/metabase http://biodatabase.org/index.php?title=Main_Page&oldid=8972 SCR_001762 MetaBase (MB) 2026-09-19 12:49:46 87
PennSeq
 
Resource Report
Resource Website
1+ mentions
PennSeq (RRID:SCR_001763) PennSeq software resource Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. isoform, gene expression, rna-seq, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: SourceForge
PMID:24362841 Free, Available for download, Freely available biotools:pennseq, OMICS_01946 https://bio.tools/pennseq SCR_001763 2026-09-19 12:49:46 4
Chilibot: Gene and Protein relationships from MEDLINE
 
Resource Report
Resource Website
10+ mentions
Chilibot: Gene and Protein relationships from MEDLINE (RRID:SCR_001705) Chilibot analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation drug, gene, literature, natural language processing, protein, text-mining, network, keyword, biological concept, graph, bio.tools is listed by: OMICtools
is listed by: 3DVC
is listed by: bio.tools
is listed by: Debian
is related to: PubMed
has parent organization: University of Tennessee Health Science Center; Tennessee; USA
PHS DA-03977 PMID:15473905 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01176, nif-0000-10196, biotools:chilibot https://bio.tools/chilibot SCR_001705 Chilibot - Mining PubMed for relationships 2026-09-19 12:49:46 33
PhosphoSitePlus: Protein Modification Site
 
Resource Report
Resource Website
1000+ mentions
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) PSP data or information resource, knowledge environment resource, portal A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
is related to: Cytoscape
is related to: ConsensusPathDB
has parent organization: Cell Signaling Technology
NCI ;
NIAAA R44 AA014848;
NIGMS R43 GM65768
PMID:22135298 Free, Freely available biotools:phosphositeplus, nif-0000-10399 https://bio.tools/phosphositeplus SCR_001837 PhosphoSitePlus, PhosphoSite 2026-09-19 12:49:48 1003
R Project for Statistical Computing
 
Resource Report
Resource Website
10000+ mentions
R Project for Statistical Computing (RRID:SCR_001905) R software resource Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. R software, statistical, computing, graphics, programming, language, bio.tools is used by: UTR
is used by: MSstats
is used by: CummeRbund
is used by: deFuse
is used by: JASP
is used by: Boruta
is used by: NMRProcFlow
is used by: PlotsOfData
is used by: rtransparent
is used by: shinyCircoss
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is affiliated with: CRAN
is affiliated with: factoextra
is affiliated with: dendsort
is affiliated with: viridis
is affiliated with: RColorBrewer
is affiliated with: statmod
is related to: Sweave
is related to: rOpenSci
is related to: R Manuals
is related to: Bioconductor
is related to: ggplot2
is related to: madsim
is related to: Solas
is related to: braincog
is related to: clustree
is related to: PhenoSpD
is related to: geomorph
is related to: NeuroAnatomy Toolbox
is related to: dplyr
is related to: glmmADMB
is related to: clusterProfiler
is related to: ropls
is related to: mixOmics
is related to: FlowSOM
is related to: Rtsne
is related to: scran
is related to: Rsubread
is related to: riboSeqR
is related to: Biostrings
is related to: riboWaltz
is related to: GenomicFeatures
is related to: devtools
is related to: affy
is related to: affydata
is related to: Heatmapper
is related to: toxprofileR
is related to: LTRpred
is related to: RaceID
is related to: PRSice
is related to: Genomic Ranges
is related to: Goseq
is related to: GAGE
is related to: metagear
is related to: pagoda2
is related to: dndSCV
is related to: tidyr
is related to: ClustVis
is related to: IDR
is related to: NeuroAnatomy Toolbox
is related to: rjags
is related to: gProfiler2
is related to: knitr
is related to: EpiEstim
is related to: Minimum-Hypergeometric Test
is related to: Network-Based R-Statistics
is related to: seqpac
is related to: survminer
is related to: Vector Generalized Linear and Additive Models
is related to: LEA
is related to: StAMPP
is related to: Betareg
is related to: Harrell Miscellaneous
is related to: simplePHENOTYPES
is related to: Bayesian Generalized Linear Regression
is related to: ranger
is related to: h2o4gpu
is related to: ridge regression Best Linear Unbiased Prediction
is related to: Classification And Regression Training
is related to: Rphenograph
is related to: Peptides
is related to: taxize
is related to: seqinr
is related to: reshape2
is related to: monaLisa
is related to: mia
is related to: Rtsne
is related to: R package:stats-package
is related to: R package: maxstat
is related to: stats
PMID:18252159 SCR_021974, nif-0000-10474, OMICS_01147, biotools:r https://cran.r-project.org/src/base/R-3/, https://bio.tools/r SCR_001905 R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing 2026-09-19 12:49:49 52118
Pecan
 
Resource Report
Resource Website
50+ mentions
Pecan (RRID:SCR_001909) software resource A Java consistency based multiple sequence alignment software program. java, sequence, alignment, consistency, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of California at Santa Cruz; California; USA
PMID:18849524 Free, Available for download, Freely available OMICS_03739, biotools:pecan http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html, https://bio.tools/pecan SCR_001909 2026-09-19 12:49:49 51
Ray
 
Resource Report
Resource Website
1+ mentions
Ray (RRID:SCR_001916) Ray software resource Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. mpi, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:20958248
DOI:10.1089/cmb.2009.0238
Free, Available for download, Freely available OMICS_00027, biotools:ray https://bio.tools/ray, https://sources.debian.org/src/ray/ SCR_001916 Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing 2026-09-19 12:49:50 1
GATK
 
Resource Report
Resource Website
10000+ mentions
GATK (RRID:SCR_001876) GATK data analysis software, data processing software, software application, software library, software resource, software toolkit A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) gene, genetic, genomic, next-generation resequencing, bio.tools is used by: Halvade Somatic
is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: SnpEff
is related to: GATK HaplotypeCaller
is related to: GATK VariantFiltration
has parent organization: Broad Institute
PMID:21478889 Free, Available for download, Freely available nlx_154324, OMICS_00286, biotools:gatk http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit, https://bio.tools/gatk SCR_001876 Genome Analysis ToolKit 2026-09-19 12:49:49 18211
TCW
 
Resource Report
Resource Website
1+ mentions
TCW (RRID:SCR_001875) TCW software resource Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R. transcript, assembly annotation, differential expression, transcript set, ortholog, expression, linux, java, mysql, r, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Arizona; Arizona; USA
NSF IOS-1044821 PMID:23874959 Free, Available for download, Freely available OMICS_01940, biotools:tCW https://bio.tools/TCW SCR_001875 Transcriptome Computational Workbench, TCW: Transcriptome Computational Workbench 2026-09-19 12:49:49 2

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.

Can't find the RRID you're searching for? X
X
  1. NIDDK Information Network Resources

    Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.

  2. Navigation

    You are currently on the Community Resources tab looking through categories and sources that dkNET 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.

  3. Logging in and Registering

    If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.

  4. Searching

    Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:

    1. Use quotes around phrases you want to match exactly
    2. You can manually AND and OR terms to change how we search between words
    3. You can add "-" to terms to make sure no results return with that term in them (ex. Cerebellum -CA1)
    4. You can add "+" to terms to require they be in the data
    5. Using autocomplete specifies which branch of our semantics you with to search and can help refine your search
  5. Collections

    If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.

  6. Facets

    Here are the facets that you can filter the data by.

  7. Further Questions

    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.