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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.

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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
CSSP
 
Resource Report
Resource Website
10+ mentions
CSSP (RRID:SCR_012932) CSSP software resource Software for power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process. is listed by: OMICtools
has parent organization: Bioconductor
PMID:23665773 Free OMICS_00426 SCR_012932 ChIP-SEQ Statistical Power 2026-09-05 06:27:29 16
cghMCR
 
Resource Report
Resource Website
1+ mentions
cghMCR (RRID:SCR_012898) cghMCR software resource Software package that provides functions to identify genomic regions of interest based on segmented copy number data from multiple samples. is listed by: OMICtools
has parent organization: Bioconductor
OMICS_00710 SCR_012898 2026-09-05 06:27:29 5
RankProd
 
Resource Report
Resource Website
100+ mentions
RankProd (RRID:SCR_013046) RankProd software resource Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). is listed by: OMICtools
has parent organization: Bioconductor
OMICS_01313 SCR_013046 2026-09-05 06:27:31 186
MEDIPS
 
Resource Report
Resource Website
100+ mentions
MEDIPS (RRID:SCR_012996) MEDIPS software resource Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). is listed by: OMICtools
has parent organization: Bioconductor
OMICS_00613 SCR_012996 MeDIP-seq data analysis 2026-09-05 06:27:30 175
Ringo
 
Resource Report
Resource Website
10+ mentions
Ringo (RRID:SCR_012973) Ringo software resource Software package that facilitates the primary analysis of ChIP-chip data. is listed by: OMICtools
is listed by: SoftCite
has parent organization: Bioconductor
OMICS_00809 SCR_012973 2026-09-05 06:27:30 38
phyloseq
 
Resource Report
Resource Website
1000+ mentions
phyloseq (RRID:SCR_013080) phyloseq software resource Software for handling and analysis of high-throughput microbiome census data. bio.tools is used by: microViz
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
DOI:10.1371/journal.pone.0061217 OMICS_01520, biotools:phyloseq https://bio.tools/phyloseq, https://sources.debian.org/src/r-bioc-phyloseq/ SCR_013080 2026-09-05 06:27:32 3080
BayesPeak
 
Resource Report
Resource Website
10+ mentions
BayesPeak (RRID:SCR_013011) BayesPeak software resource Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. is listed by: OMICtools
has parent organization: Bioconductor
OMICS_00432 SCR_013011 BayesPeak - Bayesian Analysis of ChIP-seq Data 2026-09-05 06:27:31 13
ChIPseqR
 
Resource Report
Resource Website
ChIPseqR (RRID:SCR_013016) ChIPseqR software resource Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. is listed by: OMICtools
has parent organization: Bioconductor
OMICS_00501 SCR_013016 2026-09-05 06:27:31 0
aCGH
 
Resource Report
Resource Website
100+ mentions
aCGH (RRID:SCR_013232) aCGH software resource Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. is listed by: OMICtools
has parent organization: Bioconductor
OMICS_00698 SCR_013232 2026-09-05 06:27:34 136
Fred Hutchinson Cancer Center
 
Resource Report
Resource Website
10+ mentions
Fred Hutchinson Cancer Center (RRID:SCR_004984) Fred Hutch Cancer Research Center institution Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program. Adult cancer research and care center, UW Medicine, cancer is parent organization of: CODEHOP
is parent organization of: Coddle-Codons Optimized to Discover Deleterious LEsions
is parent organization of: Pplacer
is parent organization of: International Histocompatibility Cell and DNA Bank
is parent organization of: Bioconductor
is parent organization of: Blocks
is parent organization of: VariantAnnotation
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Scientific Imaging
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Proteomics Resource
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Research Freezers and Sample Storage Resource
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Flow Cytometry
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Specimen Processing/Research Cell Bank
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Glassware Services
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Electron Microscopy
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Experimental Histopathology Shared Resource
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Arnold Library
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Genomics Shared Resource
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Comparative Medicine
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Antibody Technology
is parent organization of: Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology
is parent organization of: Fred Hutchinson Cancer Center Therapeutic Products Core Facility
is parent organization of: Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility
is parent organization of: Fred Hutchinson Cancer Center Biostatistics Shared Resource
is parent organization of: Fred Hutchinson Cancer Center Collaborative Data Services Core Facility
is parent organization of: Fred Hutchinson Cancer Center Genomics and Bioinformatics Core Facility
is parent organization of: Fred Hutchinson Cancer Center Antibody Technology Core Facility
is parent organization of: Fred Hutchinson Cancer Center Cellular Imaging Core Facility
is parent organization of: Fred Hutchinson Cancer Center Comparative Medicine Core Facility
is parent organization of: Fred Hutchinson Cancer Center Electron Microscopy Core Facility
is parent organization of: Fred Hutchinson Cancer Center Experimental Histopathology Core Facility
is parent organization of: Fred Hutchinson Cancer Center Flow Cytometry Core Facility
is parent organization of: Fred Hutchinson Cancer Center Immune Monitoring Core Facility
is parent organization of: Fred Hutchinson Cancer Center Preclinical Imaging Core Facility
is parent organization of: Fred Hutchinson Cancer Center Preclinical Modeling Core Facility
is parent organization of: Fred Hutchinson Cancer Center Proteomics and Metabolomics Core Facility
is parent organization of: Fred Hutchinson Cancer Center Leica Center of Excellence Core Facility
is parent organization of: Fred Hutch Cancer Center Translational Pathology Core Facility
Wikidata Q1452369, , Crossref Funder ID 100005895, ISNI 0000 0001 2180 1622, nlx_94018, GRID grid.270240.3 https://ror.org/007ps6h72, https://www.fhcc.org/?_gl=1%2A1ewelpw%2A_ga%2AMTY0NDY4MTI0LjE2NTg5NDc1OTQ.%2A_ga_CMZTF4L2MS%2AMTY1ODk0NzU5NC4xLjEuMTY1ODk0ODUyNy4w SCR_004984 2026-09-05 06:30:41 10
BHC
 
Resource Report
Resource Website
BHC (RRID:SCR_006399) BHC data processing software, software application, software resource Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets. clustering, microarray is listed by: OMICtools
has parent organization: Bioconductor
PMID:19660130 GNU General Public License, v3 OMICS_02215 SCR_006399 Bayesian Hierarchical Clustering 2026-09-05 06:30:42 0
PICS
 
Resource Report
Resource Website
1+ mentions
PICS (RRID:SCR_001093) data analysis software, data processing software, sequence analysis software, software application, software resource R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. chip seq, bayes, data, r, sequence analysis software is listed by: OMICtools
is hosted by: Bioconductor
PMID:20528864 Free, Available for download, Freely available OMICS_00455 SCR_001093 Probabilistic inference of ChIP-seq 2026-09-05 06:29:53 3
Goseq
 
Resource Report
Resource Website
100+ mentions
Goseq (RRID:SCR_017052) data analysis software, data processing software, software application, software resource Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is related to: R Project for Statistical Computing
PMID:20132535 Free, Available for download, Freely available biotools:goseq https://bio.tools/goseq SCR_017052 2026-09-05 06:28:17 382
Genomic Ranges
 
Resource Report
Resource Website
1+ mentions
Genomic Ranges (RRID:SCR_017051) data analysis software, data processing software, software application, software resource, software toolkit Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is related to: R Project for Statistical Computing
NHGRI P41 HG004059;
NHGRI U41 HG004059;
NHLBI R01 HL086601;
NHLBI R01 HL093076;
NHLBI R01 HL094635
PMID:23950696 Free, Available for download, Freely available biotools:genomicranges https://bio.tools/genomicranges SCR_017051 2026-09-05 06:28:17 2
ascend
 
Resource Report
Resource Website
1+ mentions
ascend (RRID:SCR_017257) data analysis software, data processing software, software application, software resource Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: CRAN
is related to: Bioconductor
PMID:31505654 Free, Available for download, Freely available biotools:ascend https://bio.tools/ascend SCR_017257 Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression 2026-09-05 06:28:21 2
Scfind
 
Resource Report
Resource Website
1+ mentions
Scfind (RRID:SCR_017339) data or information resource, data processing software, software application, software resource Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. Single, cell, RNA-seq, data, gene, list, build, index, organize is listed by: Bioconductor
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Free, Available for download, Freely available https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind SCR_017339 2026-09-05 06:28:23 1
epialleleR
 
Resource Report
Resource Website
1+ mentions
epialleleR (RRID:SCR_023913) software resource, software toolkit Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data. BAM files, binary alignment map files, allele specific methylation analysis, methylation sequencing data, next generation sequencing data, hypermethylated variant epiallele frequencies calling, is listed by: Bioconductor K.G.Jebsen Foundation ;
Norwegian Cancer Society ;
Norwegian Research Council
DOI:10.1101/2022.06.30.498213 Free, Available for download, Freely available https://github.com/BBCG/epialleleR SCR_023913 2026-09-05 06:31:02 1
CRCView
 
Resource Report
Resource Website
CRCView (RRID:SCR_007092) CRCView analysis service resource, data analysis service, production service resource, service resource Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: Bioconductor
is related to: Gene Ontology
has parent organization: University of Michigan; Ann Arbor; USA
University of Michigan; Michigan; USA ;
Institutional Fund ;
NIH U013422;
NIAID 1R21AI057875-01
PMID:17485426 Registration required biotools:crcview, nlx_99864 https://bio.tools/crcview http://helab.bioinformatics.med.umich.edu/crcview/ SCR_007092 Chinese Restaurant ClusterView 2026-09-05 06:31:38 0
iontree
 
Resource Report
Resource Website
iontree (RRID:SCR_002813) software resource Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
PMID:24958264 Free, Freely available, Available for download OMICS_02656, biotools:iontree https://bio.tools/iontree SCR_002813 iontree: Data management and analysis of ion trees from ion-trap mass spectrometry 2026-09-05 06:30:19 0
Extending Guilt by Association by Degree
 
Resource Report
Resource Website
1+ mentions
Extending Guilt by Association by Degree (RRID:SCR_018427) EGAD data analysis software, data processing software, software application, software resource, software toolkit Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks. Extending guilt, association by degree, functional properties calculation, guilt network, association method, functional analysis, gene network is listed by: Bioconductor Free, Available for download, Freely available SCR_018427 EGAD Bioconductor, Extending guilt by association by degree 2026-09-05 06:28:36 6

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