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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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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