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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 Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Qvalue
 
Resource Report
Resource Website
10+ mentions
Qvalue (RRID:SCR_001073) software resource, software application, data analysis software, data processing software R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining. p value, false positive, null hypothesis, genomics, brain imaging, astrophysics, data mining, r, visualization is listed by: OMICtools
is hosted by: Bioconductor
Free, Available for download, Freely available OMICS_00624 https://github.com/jdstorey/qvalue SCR_001073 2026-02-12 09:43:05 31
SoftCite
 
Resource Report
Resource Website
SoftCite (RRID:SCR_024411) project portal, software resource, knowledge base, data or information resource, portal Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale. Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature, lists: ProteinPilot
lists: ROCit
lists: survivalROC
lists: GIFT
lists: PyWavelets
lists: pRRophetic
lists: GOplot
lists: Rgdal
lists: riskRegression
lists: RNAfold
lists: RNALocate
lists: pyPCcazip
lists: ScanProsite
lists: RapGreen
lists: ABySS
lists: AMBER
lists: ANNOVAR
lists: ASAP
lists: ASPicDB
lists: AStalavista
lists: ATSAS
lists: Alien hunter
lists: Adobe Photoshop
lists: Affymetrix
lists: Augustus
lists: Argus
lists: Adobe Illustrator
lists: ART
lists: AutoDock Vina
lists: AutoDock
lists: ANALYZE
lists: BLASTClust
lists: arrayQualityMetrics
lists: BLASTN
lists: BLASTX
lists: BLASTP
lists: Bowtie
lists: Autogrid
lists: BRB-ArrayTools
lists: BEDTools
lists: BWA
lists: BioEdit
lists: BRASS
lists: Bioconductor
lists: BioExtract
lists: BaCelLo
lists: BioMoby
lists: Brain Extraction Tool
lists: Bowtie 2
lists: BoxPlotR
lists: biomaRt
lists: BioPerl
lists: CANGS
lists: CFX Manager
lists: CEAS
lists: BlobFinder
lists: CLC Genomics Workbench
lists: BREAKDANCER
lists: CASAVA
lists: CLC Main Workbench
lists: ClustalW
lists: Clustal W2
lists: ComBat
lists: CCP4
lists: Blender
lists: Coot
lists: CGView
lists: COMSOL Multiphysics
lists: CTFFIND
lists: CalcuSyn
lists: ChIPpeakAnno
lists: Chimera
lists: CVODE
lists: DAVID
lists: Cufflinks
lists: caret
lists: ClueGO
lists: Cluster
lists: Clocklab
lists: DIANA-mirPath
lists: Cytoscape
lists: EMAN
lists: E-Prime
lists: DESeq2
lists: Definiens Developer XD
lists: Eigensoft
lists: EMBOSS
lists: Ensembl
lists: DIALIGN
lists: Design-Expert
lists: EndNote
lists: CMAP
lists: EEGLAB
lists: CMap
lists: Epi Info
lists: FASTA
lists: Ensembl Genome Browser
lists: Epik
lists: FACS
lists: FCS Express
lists: Flowlogic
lists: FSL
lists: FLASH
lists: FATCAT
lists: FastQC
lists: G*Power
lists: GOLD
lists: FGENESH
lists: FreeSurfer
lists: FlowJo
lists: GeneTools
lists: Galaxy
lists: GATK
lists: ELDA
lists: GraphPad
lists: GRADEpro
lists: Fiji
lists: Gblocks
lists: FigTree
lists: GENIE
lists: GBrowse
lists: Gemma
lists: GeneChip Operating Software
lists: GeneMapper
lists: GeneMarker
lists: GenABEL
lists: GenePattern
lists: GraphPad Prism
lists: GenePix Pro
lists: Google
lists: Genesis
lists: Hologic
lists: GeneSpring GX
lists: GeneVenn
lists: HaploReg
lists: Google Scholar
lists: HALO
lists: Gwyddion
lists: IMAGIC
lists: HKL-2000
lists: Glide
lists: Glimmer
lists: I-TASSER
lists: GenomeStudio
lists: IMOD
lists: Haploview
lists: Hmmer
lists: Hydra
lists: IUPRED
lists: HomeCageScan
lists: Geneious
lists: IGOR Pro
lists: IMPUTE
lists: Infernal
lists: Image-Pro Plus
lists: JASP
lists: LSM Image Examiner
lists: Imaris
lists: Image Pro Plus
lists: ImageQuant
lists: ImageJ
lists: Integrative Genomics Viewer
lists: jcvi
lists: InterProScan
lists: KaleidaGraph
lists: Ligprep
lists: Heidelberg Eye Explorer
lists: JMP
lists: Ingenuity Pathways Knowledge Base
lists: Leica QWin
lists: JCB DataViewer
lists: Jalview
lists: LigandScout
lists: Ingenuity Pathway Analysis
lists: LabView
lists: Kepler
lists: MAFFT
lists: Jmol
lists: ImageScope
lists: MACS
lists: Maq
lists: MUMmer
lists: MATLAB
lists: Mimics
lists: MACH
lists: MCODE
lists: Mascot
lists: Maestro
lists: MSQuant
lists: MediaWiki
lists: MINC
lists: MRIcron
lists: MOE
lists: ModFit LT
lists: LIMMA
lists: MassLynx
lists: mitopred
lists: MrBayes
lists: MolProbity
lists: MUSCLE
lists: MutationAssessor
lists: MaxQuant
lists: Minitab
lists: MODELLER
lists: MetaboAnalyst
lists: MedCalc
lists: Origin
lists: MPlus
lists: MutationTaster
lists: MuTect
lists: Multi Gauge
lists: NIA Array Analysis
lists: NIH Image
lists: Phenix
lists: MycoBank
lists: OpenClinica
lists: Nexus
lists: OMTools
lists: NIS-Elements
lists: PAST
lists: NVivo
lists: PRISM (Stanford database)
lists: Metscape
lists: PROCHECK
lists: oligo
lists: OpenEpi
lists: Pathway Commons
lists: Nanoparticle Tracking Analysis
lists: Openlab
lists: PLINK
lists: PAUP
lists: NONMEM
lists: PREFAB
lists: NetworkX
lists: PeptideProphet
lists: Primer Designer
lists: PhyML
lists: PASS
lists: PyMOL
lists: PSIPRED
lists: PROFILER
lists: PHYLIP
lists: Phobius
lists: Prime
lists: Phyutility
lists: Picard
lists: ProteinProphet
lists: Phaser
lists: ProSAS
lists: PostgreSQL
lists: Primer-BLAST
lists: ProteinLynx Global Server
lists: QUANTO
lists: Primer Express
lists: Primer3Plus
lists: ProtTest
lists: ProbCons
lists: Primer3
lists: Poretools
lists: Protein preparation Wizard
lists: QmRLFS-finder
lists: PicTar
lists: RevMan
lists: Pipeline Pilot
lists: QIIME
lists: PRISMA
lists: REDCap
lists: RAxML
lists: Proteome Discoverer
lists: Research Randomizer
lists: SPARTAN
lists: SPSS
lists: RNAstructure
lists: Refmac
lists: QuantPrime
lists: Prodigal
lists: RepeatModeler
lists: Ringo
lists: SQLite
lists: SAGE
lists: Rhinoceros
lists: SAMTOOLS
lists: SPAdes
lists: RepeatMasker
lists: SEDFIT
lists: STATISTICA
lists: RNAhybrid
lists: SlideBook
lists: STRUCTURE
lists: SABmark
lists: SPM
lists: Stata
lists: RStudio
lists: SciPy
lists: Scion Image
lists: Simulink
lists: TAGGER
lists: TopHat
lists: SAM
lists: ShortRead
lists: SIFT
lists: SCAN
lists: SignalP
lists: Scopus
lists: Strelka
lists: Trans-ABySS
lists: Statgraphics Centurion
lists: T-Coffee
lists: Statistical Analysis System
lists: TargetScan
lists: UCHIME
lists: Sequencher
lists: SigmaStat
lists: UCSC Genome Browser
lists: affy
lists: Taverna
lists: Stereo Investigator
lists: Trimmomatic
lists: Vmatch
lists: WFU PickAtlas
lists: SigmaPlot
lists: X!Tandem
lists: STAR
lists: TASSEL
lists: SyStat
lists: WEBLOGO
lists: UCSF Chimera
lists: TreeView
lists: pheatmap
lists: WinWCP
lists: microRNA.org
lists: glmnet
lists: Phenix.refine
lists: BASE
lists: beadarray
lists: RMS
lists: lumi
lists: Web of Science
lists: minfi
lists: geNORM
lists: WU-BLAST
lists: WinBUGS
lists: SPP
lists: tRNAscan-SE
lists: WebPlotDigitizer
lists: qBasePLUS
lists: Matplotlib
lists: TreeBASE
lists: pClamp
lists: TBLASTN
lists: igraph
lists: V3D
lists: survival
lists: miRanda
lists: piRNABank
lists: topGO
lists: NGmerge
lists: OMNISEC
lists: NOTUNG
lists: OpenBUGS
lists: Optimization Toolbox
lists: ProgRes Capture Pro
lists: Ocular
lists: Umediation
lists: Nano Measurer
lists: PHYLDOG
lists: VSEARCH
lists: WinNonlin
lists: WHONET
lists: ToposPro
lists: Treerecs
lists: Agilent Seahorse Wave
lists: SimPhy
lists: TomoStudio
lists: Mutation Assessor
lists: Stem
lists: SRAMP
lists: CRISPResso2
lists: geepack
lists: Evalue
lists: DAGitty
lists: FastMulRFS
lists: ggridges
lists: gamm4
lists: AutoRT
lists: CopyKAT
lists: Inference of CRISPR Edits
lists: classInt
lists: ASTRAL-Pro
lists: maftools
lists: mitml
lists: CMplot
lists: MetaPSICOV
lists: LaCyTools
lists: MADOKA
lists: Kaplan Meier Plotter
lists: IntFOLD
lists: ModFOLD
lists: lDDT
has parent organization: University of Texas at Austin; Texas; USA
Sloan Foundation DOI:10.1002/asi.24454 Free, Available for download, Freely available https://github.com/softcite/softcite_dataset_v2
https://zenodo.org/record/7995565
SCR_024411 Software Citation 2026-02-12 09:48:13 0
HTqPCR
 
Resource Report
Resource Website
50+ mentions
HTqPCR (RRID:SCR_003375) HTqPCR software application, software resource, data processing software Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). data import, differential expression, gene expression, microtitre plate assay, multiple comparison, preprocessing, quality control, visualization, qpcr, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
has parent organization: European Bioinformatics Institute
PMID:19808880 Free, Available for download, Freely available biotools:htqpcr, OMICS_02314 https://bio.tools/htqpcr SCR_003375 HTqPCR - Automated analysis of high-throughput qPCR data 2026-02-12 09:43:35 74
microbiome
 
Resource Report
Resource Website
1+ mentions
microbiome (RRID:SCR_024699) software toolkit, software resource Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data. amplicon sequencing data, microbiome analysis, is listed by: Bioconductor Free, Available for download, Freely available https://microbiome.github.io/tutorials/
https://github.com/microbiome/microbiome/
SCR_024699 2026-02-12 09:48:03 9
tximport
 
Resource Report
Resource Website
50+ mentions
tximport (RRID:SCR_016752) software resource, software application, data analysis software, data processing software Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
works with: edgeR
works with: DESeq2
SNSF 143883;
European Commission ;
NCI T32 CA009337
DOI:10.12688/f1000research.7563.1 Free, Available for download, Freely available biotools:tximport https://bioconductor.org/packages/tximport/
https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
https://github.com/F1000Research/tximport
https://bio.tools/tximport
https://zenodo.org/record/35123#.W_w3behKiM8 SCR_016752 tximport v1.4.0 2026-02-12 09:46:37 91
MetaNeighbor
 
Resource Report
Resource Website
10+ mentions
MetaNeighbor (RRID:SCR_016727) software resource, software application, data analysis software, data processing software Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting. quantify, cell, type, replicability, dataset, access, cell, type, identity, functional, random, gene is used by: BICCN
is listed by: Bioconductor
is listed by: OMICtools
Free, Available for download, Freely available https://github.com/maggiecrow/MetaNeighbor
https://github.com/gillislab/MetaNeighbor
SCR_016727 2026-02-12 09:46:55 49
RMassBank
 
Resource Report
Resource Website
1+ mentions
RMassBank (RRID:SCR_002797) software application, workflow software, software resource, data processing software Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics is listed by: OMICtools
has parent organization: Bioconductor
Free, Freely available, Available for download OMICS_02657 SCR_002797 2026-02-12 09:43:27 6
variancePartition
 
Resource Report
Resource Website
50+ mentions
variancePartition (RRID:SCR_019204) software resource, software application, data analysis software, data processing software, data analytics software Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools is listed by: Bioconductor
is listed by: bio.tools
is listed by: Debian
is related to: CRAN
NHLBI U01 HL107388;
Icahn School of Medicine at Mount Sinai
PMID:27884101 Free, Available for download, Freely available biotools:variancepartition https://bio.tools/variancepartition SCR_019204 2026-02-12 09:47:04 52
SynergyFinder
 
Resource Report
Resource Website
500+ mentions
SynergyFinder (RRID:SCR_019318) software toolkit, software resource, software application, data processing software, data visualization software Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations. Synergy scores, drug combinations, popular synergy scoring models, dimensional interaction surface, dose matrix, bio.tools is listed by: Bioconductor
is listed by: bio.tools
is listed by: Debian
is related to: SynergyFinder web application
DOI:10.1007/978-1-4939-7493-1_17 Free, Available for download, Freely available biotools:synergyfinder https://bio.tools/synergyfinder SCR_019318 synergyfinder 2026-02-12 09:47:12 510
fgsea
 
Resource Report
Resource Website
100+ mentions
fgsea (RRID:SCR_020938) software resource, software application, data analysis software, data processing software Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Gene set enrichment analysis, preranked gene set, multiple hypothesis correction, bio.tools is listed by: Bioconductor
is listed by: bio.tools
is listed by: Debian
DOI:10.1101/060012 Free, Available for download, Freely available biotools:fgsea https://github.com/ctlab/fgsea/
https://bio.tools/fgsea
SCR_020938 fast gene set enrichment analysis, Fast Gene Set Enrichment Analysis, FGSEA 2026-02-12 09:47:42 185
CiteFuse
 
Resource Report
Resource Website
1+ mentions
CiteFuse (RRID:SCR_019321) software resource, software application, data analysis software, data processing software Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools is listed by: Bioconductor
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Sydney; Sydney; Australia
PMID:32353146 Free, Available for download, Freely available biotools:citefuse https://bioconductor.org/packages/CiteFuse/
https://github.com/SydneyBioX/CiteFuse/
http://shiny.maths.usyd.edu.au/CiteFuse/
https://bio.tools/CiteFuse
SCR_019321 Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse 2026-02-12 09:47:07 2
ggtree
 
Resource Report
Resource Website
50+ mentions
ggtree (RRID:SCR_018560) software application, data processing software, software resource, data visualization software Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools is listed by: CRAN
is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
Seed Funding Programme for Basic Research DOI:10.1111/2041-210X.12628 Free, Available for download, Freely available biotools:ggtree https://bio.tools/ggtree SCR_018560 2026-02-12 09:46:53 54
minet
 
Resource Report
Resource Website
minet (RRID:SCR_018661) software toolkit, software resource, network analysis software, software application, data analysis software, data processing software Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Bioconductor
has parent organization: Free University of Brussels; Brussels; Belgium
Communaute Francaise de Belgique PMID:18959772 Free, Available for download, Freely available biotools:minet http://minet.meyerp.com/
https://bio.tools/minet
SCR_018661 Mutual Information NETworks 2026-02-12 09:46:54 0
scTHI
 
Resource Report
Resource Website
1+ mentions
scTHI (RRID:SCR_018918) scTHI software resource, software application, data analysis software, data processing software Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment. Ligand receptor, active pair, active pair ligand receptor, single cell, tumor interaction, tumor microenvironment, cells clasification is listed by: Bioconductor Free, Available for download, Freely available SCR_018918 2026-02-12 09:47:06 1
org.Hs.eg.db
 
Resource Report
Resource Website
10+ mentions
org.Hs.eg.db (RRID:SCR_024739) software toolkit, software resource Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers. simple mapping of Entrez Gene identifiers, GenBank accession numbers, is listed by: Bioconductor Free, Available for download, Freely available SCR_024739 2026-02-12 09:48:19 24
combi
 
Resource Report
Resource Website
1+ mentions
combi (RRID:SCR_024986) software toolkit, software resource Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality. integrate omics data for visualization, simultaneous exploration, multiple datasets, visual integration, joint visualization, including sample variables in analysis, is listed by: Bioconductor Johnson and Johnson PMID:33575602 Free, Available for download, Freely available SCR_024986 Compositional Omics Model-Based Integration 2026-02-12 09:48:51 1
org.Rn.eg.db
 
Resource Report
Resource Website
1+ mentions
org.Rn.eg.db (RRID:SCR_018358) software application, software resource Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers. Genome annotation, rat, mapping, Entrez Gene identifier is listed by: Bioconductor Free, Available for download, Freely available SCR_018358 2026-02-12 09:46:50 1
ChIPseeker
 
Resource Report
Resource Website
100+ mentions
ChIPseeker (RRID:SCR_021322) software toolkit, software resource Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes. Retrieve nearest genes around peak, annotate genomic region of peak, overlap estimate significance, ChIP peak data sets uses: Gene Expression Omnibus (GEO)
is listed by: Bioconductor
PMID:25765347 Free, Available for download, Freely available SCR_021322 2026-02-12 09:47:18 290
CATALYSTLite
 
Resource Report
Resource Website
CATALYSTLite (RRID:SCR_017126) service resource, analysis service resource, production service resource, data analysis service Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package. interactive, Shiny, website, application, interface, mass, cytometry, data, processing, pipeline is used by: CATALYST
is related to: Bioconductor
has parent organization: University of Zurich; Zurich; Switzerland
Free, Freely available SCR_017126 2026-02-12 09:47:01 0
EGSEA
 
Resource Report
Resource Website
50+ mentions
EGSEA (RRID:SCR_015036) source code, software resource, software toolkit Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. gene set, rna sequencing, analysis method, r package, bio.tools is listed by: Debian
is listed by: bio.tools
is hosted by: Bioconductor
Victorian State Government Operational Infrastructure Support ;
Australian Government NHMRC IRIISS ;
NHMRC GNT1050661;
NHMRC GNT1045936;
NHMRC GNT1057854;
NHMRC GNT1104924
PMID:27694195 Free, Available for download biotools:egsea https://bio.tools/egsea SCR_015036 Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses 2026-02-12 09:46:24 62

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