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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Cross Validation Resource Report Resource Website |
Cross Validation (RRID:SCR_000702) | service resource, training service resource | A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation. | model, modeling, training, data, holdout, k fold, cross, validation | has parent organization: Carnegie Mellon University; Pennsylvania; USA | nlx_19901 | SCR_000702 | 2026-02-16 09:45:19 | 0 | ||||||||||
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Bioconductor Resource Report Resource Website 10000+ mentions |
Bioconductor (RRID:SCR_006442) | software repository, software resource, software toolkit | Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. | catalog, analysis, genomic, metadata, comprehension, statistical, data |
lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq |
Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708 |
PMID:15461798 | Free, Freely available | OMICS_01759, nif-0000-10445 | SCR_006442 | 2026-02-16 09:46:43 | 22974 | |||||||
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OpenBehavior Resource Report Resource Website 1+ mentions |
OpenBehavior (RRID:SCR_015938) | OB | software repository, software resource | Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects. | software, data, hardware, animal, behavior, cognition, cognitive, analysis, processing |
lists: Feeding Experimentation Device project lists: Bpod lists: SLEAP, LEAP and MotionMapper project lists: Social LEAP lists: MotionMapper lists: Behavioral Segmentation of Open-field in DeepLabCut project lists: DeepBehavior project lists: BonZeb project lists: D-Track project lists: Online Animal Tracker project lists: Locomouse project lists: openEyeTrack project lists: DeepPoseKit project lists: DeepFly3D project lists: neurotic project lists: Rodent Arena Tracker project lists: Open Source Whisking Video Database portal lists: Simple Behavior Analysis project lists: OpenMonkeyStudio project lists: FaceSync project lists: Online Animal Tracker lists: DeepBehavior lists: BonZeb lists: Behavioral Segmentation of Open-field in DeepLabCut lists: FaceSync lists: LocoMouse lists: DeepPoseKit lists: openEyeTrack lists: D-Track lists: Simple Behavior Analysis lists: DeepFly3D lists: Open Source Whisking Video Database lists: neurotic lists: Low Cost Open Source Eye Tracking project lists: Stytra project lists: Calcium ActiVity Explorer project lists: idtracker.ai project lists: Live Mouse Tracker project lists: ToxTrac project lists: Picamera project lists: EthoScopes project lists: Worm Behavior Platform project lists: KineMouse Wheel project lists: Mousecam project lists: M-Track project lists: ezTrack project lists: FaceMap project lists: Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project lists: ZebraTrack project lists: LocoWhisk project lists: EthoWatcher project lists: Skinner Box project lists: Behavioral Observation Research Interactive Software project lists: Pyper project lists: Automated Rodent Tracker project lists: LinCoM project lists: Bonsai project lists: Quantifying Animal Movement from Pre-recorded Videos project lists: Platform for Acoustic STArtle project lists: Joystick project lists: 3DTracker project lists: AutoPilot project lists: PiDose project lists: DeepSqueak project lists: Rigbox project lists: Catalepsy Bar project lists: Dual port Lick Detector project lists: Pathfinder project lists: Actifield project lists: Rodent Activity Detector project lists: flyPAD project lists: Automated Home Cage Rodent Two bottle Choice Test project lists: MedParse project lists: Voluntary Access Static Incapacitance Chamber project lists: Laubach Lab GitHub Repository project lists: BPM Biosignals project lists: Automated mouse homecage two bottle choice test project lists: Mousetrap project lists: Autoreward2 project lists: Optimouse project lists: Hao Chen Lab Repository project lists: AutonoMouse project lists: Spike Forest project lists: Closed Loop System project lists: ArduiPod Box project lists: Oculomatic Eye Tracking project lists: Ultrasonic Vocalizations Detector project lists: Attys project lists: Calcium Imaging data Analysis project lists: Feldman Lab Lickometer project lists: MNE Scan project lists: Open Source platform for Sensory Tasks project lists: Scintillate project lists: Pypreclin project lists: Wave Surfer project lists: An open source motorized swivel for in vivo neural and behavioral recordings project lists: Toolboxes for Spike and LFP Analysis project lists: BrainGlobe project lists: UCLA Miniscope project lists: Cerebro Wireless Optogenetic System project lists: Home Cage Automated Skilled Reaching Apparatus project lists: Open-tES project lists: Capactive Touch Sensor project lists: CapTouch project lists: Two Armed Bandit Task project lists: Novel Gustometer for Human Taste Research project lists: OpenVape project lists: Calcium ActiVity Explorer lists: Pi Virtual Reality System project lists: BonVision project lists: FinchScope project lists: Mousecam lists: ezTrack lists: DIY-NAMIC project lists: Precision Syringe Pump Controller project lists: idtracker.ai lists: Stytra lists: EthoScopes lists: Worm Behavior Platform lists: Ardbark project lists: FaceMap lists: M-Track lists: ToxTrac lists: Pyper lists: Low Cost Open Source Eye Tracking lists: Automated Rodent Tracker lists: Live Mouse Tracker analysis lists: LinCoM lists: Skinner Box lists: 3DTracker lists: Pathfinder lists: Behavioral Observation Research Interactive Software lists: MNE Scan lists: Quantifying Animal Movement from Pre-recorded Videos lists: Rigbox lists: Platform for Acoustic STArtle lists: DeepSqueak lists: Oculomatic lists: Wave Surfer lists: EthoWatcher lists: MedParse lists: Bonsai lists: Scintillate lists: AutoPilot lists: Spike Forest lists: flyPAD lists: Optimouse lists: Calcium Imaging data Analysis lists: BonVision lists: Dual Port Lick Detector lists: Pypreclin lists: ACRoBaT lists: Visual stimulator with customizable light spectra lists: ToneBox lists: 3DOC lists: MouseBytes lists: Touchscreen Cognition lists: FreemoVR project lists: Modular Automated Platform for Large Scale Experiments project lists: OpenFeeder lists: SnackClock lists: SignalBuddy lists: ArControl project lists: Airtrack lists: Teensy-Based Interface project lists: Autonomous Training of a Forelimb Motor Task project lists: Ratcave project lists: DIY Rodent Running Disk lists: Moving Wall Box lists: Operant Box for Auditory Tasks project lists: Camera Control project lists: FlyPi lists: CerebraLux lists: Automated Home-Cage Functional Imaging project lists: Pearce Lab Syringe Pump project lists: Craniobot project lists: PhotometryBox lists: Pulse Pal project lists: NINscope lists: Nose Poke Device lists: pyControl project lists: OpenMV project lists: Rodent Operant Bucket project lists: Tetroplater lists: OpenSpritzer lists: Argus lists: NeRD lists: PRiED lists: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project lists: MouseMove project lists: Eco-HAB lists: Homecage Task Training and Mesoscale Imaging project lists: Microwave based Homecage Motion Detector project lists: CHEndoscope lists: Robotic Flower System for Bee Behavior project lists: TRIO Platform lists: A Head Mounted Multi Camera System for Freely Moving Mice project lists: Ratcave lists: 4 Port Nose Poke lists: An Opensource lickometer and microstructure analysis program lists: Automated Classification of Self-grooming in Mice project lists: FreemoVR lists: ArControl lists: Visual Discrimination with an iPad lists: Teensy-Based Interface lists: Operant Box for Auditory Tasks lists: Autonomous Training of a Forelimb Motor Task lists: 3D Printed Headcap and Microdrive lists: poke device arduino lists: MouseBytes lists: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology lists: Rodent Operant Bucket lists: Camera Control lists: linear actuator lists: Modular Automated Platform for Large Scale Experiments lists: pyControl lists: Argus lists: NINscope software lists: OpenMV lists: MouseMove lists: chendoscope lists: craniobot lists: Pulse Pal lists: Automated Home-Cage Functional Imaging lists: AutoHeadFix lists: SpikeGadgets lists: Open Ephys lists: MRI-stereoscope project lists: AutomaticSleepScoringTool lists: Pi-based Remote Acquisition Technology for Motion Capture project lists: Pi-based Remote Acquisition Technology for Motion Capture lists: Brainrender lists: TetrODrive lists: COMPASS lists: Cellpose lists: OORTT lists: DBscorer lists: GazeMetrics lists: AutoStereota lists: FlyBrainLab lists: pyOS-5 project lists: Pyneal lists: pyOS-5 lists: Atlas Based Analysis lists: VocalMat lists: DABEST lists: Raspberry Pi based auditory stimulus generator lists: Pain Assessment at Withdrawal Speeds lists: Florida research open source synchronization tool lists: Permuco lists: LED Matrix Stimuli lists: Mouse Action Recognition System lists: Behavior Ensemble and Neural Trajectory Observatory lists: Neonatal Stereotaxic Mouse Adaptor lists: MARS Developer lists: EZcalcium lists: MRI Compatible Microdrive lists: GuPPy lists: DeepEthogram lists: Pycro Manager lists: DeepBhvTracking lists: TweetyNet lists: OpenPose lists: TRex lists: SIPEC lists: Closed Loop Automated Reaching Apparatus lists: Timed pressure control hardware and software for delivery of air mediated distensions in animal models lists: CellExplorer lists: DLStream lists: SipperViz lists: Variational Embedding of Animal Motion lists: SHARCQ lists: PavCA project lists: GoFish Ajuwon etal 2022 lists: LED Zappelin’ lists: Minian lists: Modular LED Displays project lists: OpenSync lists: USVCAM lists: Histological E data Registration in rodent Brain Spaces lists: Pi USB Cam project lists: 3D Printed Superfusion Chamber lists: pyPhotometry lists: Rtrack lists: ColonyTrack lists: Anipose lists: LiftPose3D lists: DANNCE lists: DeepLabCut Project lists: ACTman lists: Raspberry Pi Grating lists: Falcon lists: OpBox lists: Mouse Behavioral Analysis Toolbox lists: Pynapple lists: Wheel Running Activity acQuisition lists: CaT-z lists: M3 Platform lists: Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory lists: Rasberry rat lists: RodentJoystick lists: tmilltracker lists: 3D Printed Multi Pump System lists: BehaviorDEPOT lists: Open Face Homecage Running Wheel lists: RatHeadphones lists: RatInABox lists: LabNet lists: JAX Animal Behavior System lists: AnimalTA lists: Mousebytes lists: Lick Instance Quantifier Home cage Device lists: B-CALM lists: Freibox lists: commutator lists: Customized Guide Cannulas lists: BrainWAVE lists: Brainways lists: LFP Monitoring lists: PyMouseTracks lists: Lightning Pose lists: Customizable Multielectrode Array lists: Live Mouse Tracker Toolkit Analysis lists: HFOApp lists: Synaptic Vesicles Detection lists: Pipette Finding CNN lists: 3DP Gustometer lists: SEB3R lists: Lickometer Box lists: Custom-fitting-of-implants lists: Markerless Mouse Tracking for Social Experiments lists: FARESHARE lists: HERBs lists: E-Scope lists: PyBehave lists: ReachOut lists: One-rat Turnstile lists: TD_Drive lists: Holeboard lists: SaLSa lists: ghostipy lists: DREAM implant lists: HSSM lists: High-Precision Optical Fiber-Based Lickometer lists: NC4gate lists: ArUco lists: STPoseNet lists: Bell Jar lists: Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats |
Public | SCR_015938 | 2026-02-16 09:48:58 | 4 | |||||||||
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National Institute on Drug Abuse Center for Genetic Studies Resource Report Resource Website 1+ mentions |
National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) | NIDA Center for Genetic Studies | data set, data repository, storage service resource, service resource, data or information resource | Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website. | drug abuse, family, family structure, genetic analysis, genetics, addiction, age, biomaterial, cell line, citation, clinical, clinical status, data, diagnosis, dna, genotyping, human, mental disorder, mutation analysis, phenotype, publications, sex, clinical data, genotype, gene, GWAS |
is recommended by: National Library of Medicine is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIH Data Sharing Repositories has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Rutgers University; New Jersey; USA |
NIDA ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00181 | https://zork5.wustl.edu//nida/ | http://zork.wustl.edu/nida/ | SCR_013061 | National Institute of Drug Abuse (NIDA) Human Genetics Initiative, NIDA Center for Genetic Studies | 2026-02-16 09:48:20 | 6 | ||||
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LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | software application, data processing software, data analytics software, data analysis software, software resource | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | 2026-02-16 09:49:17 | 29 | ||||||||
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HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | data processing software, software application, software resource, workflow software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
France Genomique National infrastructure ; Labex Deep ; European Research Coucil ; ERC Advanced Investigator award ; European Commission ; ABS4NGS project ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes ; Howard Hughes Medical Institute |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | 2026-02-16 09:49:17 | 206 | ||||||
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tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | software toolkit, data analysis service, analysis service resource, software resource, production service resource, service resource | Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | 2026-02-16 09:49:07 | 11 | |||||||||||
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Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | software application, data processing software, software toolkit, data visualization software, software resource | Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals. | process, visualise, EEG, MEG, data, neurophysiological, signal, brain, neuroscience | is related to: MATLAB | Free, Available for download, Freely available | https://www.letswave.org/ | SCR_016414 | 2026-02-16 09:49:01 | 17 | |||||||||
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TSDiffAna Resource Report Resource Website 1+ mentions |
TSDiffAna (RRID:SCR_016656) | software application, data processing software, data analysis software, image analysis software, software resource | Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries. | SPM, statistical, parametiric, mapping, slicewise, scan, difference, standard, deviation, quality, image, neuroimaging, data |
has parent organization: University College London; London; United Kingdom is provided by: SPM |
Free, Available for download, Freely available | https://sourceforge.net/projects/tsdiffana.spmtools.p/ | SCR_016656 | 2026-02-16 09:49:04 | 2 | |||||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | software application, data processing software, software toolkit, image processing software, image analysis software, software resource | Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science works with: VisuAlign |
Free, Available for download, Freely available | SCR_017183 | Neuroimaging utilities | 2026-02-16 09:49:11 | 25 | ||||||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | organization portal, data repository, database, storage service resource, topical portal, portal, service resource, data or information resource, disease-related portal | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1 https://commonfund.nih.gov/kidsfirst |
SCR_016493 | Data Resource Portal | 2026-02-16 09:49:02 | 3 | ||||
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Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | data analysis service, analysis service resource, web application, software resource, production service resource, service resource | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele https://bio.tools/nephele |
SCR_016595 | 2026-02-16 09:49:04 | 27 | ||||||
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Cyflogic Resource Report Resource Website 10+ mentions |
Cyflogic (RRID:SCR_016635) | software application, data processing software, software toolkit, data analysis software, software resource | Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics. | flow, cytometry, data, analysis, CyFlo Ltd., dot, plot, histogram, statistics | PMID:23839300 | Commercially available, Free for non-commercial research use only and not for use in diagnostic or therapeutic procedures | SCR_016635 | 2026-02-16 09:49:04 | 25 | ||||||||||
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PASC Resource Report Resource Website 1+ mentions |
PASC (RRID:SCR_016642) | PASC | web service, analysis service resource, data access protocol, database, software resource, production service resource, service resource, data or information resource | Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. | analysis, pairwise, identity, distribution, viral, family, sequence, classification, data, taxonomy | has parent organization: NCBI | National Library of Medicine | PMID:25119676 | Free, Public | SCR_016642 | PAirwise Sequence Comparison | 2026-02-16 09:49:04 | 4 | ||||||
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SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | web service, data access protocol, database, software resource, data or information resource | Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. | collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome | Swiss National Science Foundation ; Swiss Institute of Bioinformatics |
PMID:27899579 | Free, Freely available | SCR_016885 | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-02-16 09:49:07 | 7 | |||||||
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University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility Resource Report Resource Website |
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) | University of Manitoba BIT Core Facility | core facility, access service resource, data analysis service, analysis service resource, software resource, production service resource, service resource, data or information resource | BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management. | bioinformatics, genome, assembly, microarray, transcriptomics, pathway, data, analysis, management | Restricted | SCR_017177 | University of Manitoba, BIT, Bio Information Technologies Lab, Fritensky Lab, Canada, Department of Plant Science | 2026-02-16 09:49:11 | 0 | |||||||||
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Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | data set, project portal, database, portal, data or information resource | Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data. | Spienza University of Rome, Cineca, RNA seq, transcriptome, data, brain, mouse, stress, gene, expresison | Free, Available for download, Freely available | SCR_017572 | 2026-02-16 09:49:16 | 1 | |||||||||||
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | data analysis service, analysis service resource, web application, software resource, production service resource, service resource, data or information resource | Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | creating, metadata, analysis, annotated, gene, expression, data, compendia, human, mouse |
uses: Gene Expression Omnibus has parent organization: NIAID |
PMID:27323300 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016604 | OMics Compendia Commons | 2026-02-16 09:49:04 | 1 | |||||||
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Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | software application, data processing software, data analysis software, narrative resource, workflow, training material, software resource, data or information resource | Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. | Epigenomic, analysis, pipeline, ChIP-Seq, RNA-Seq, data, Galaxy, Jupyter, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Estatal de Investigación of Spain SEV-2016-0672 (2017-2021) | Free, Available for download, Freely available | biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter | https://zenodo.org/record/3298029 https://bio.tools/Epigenomics_Workflow_on_Galaxy_and_Jupyter |
SCR_017544 | REA pipeline | 2026-02-16 09:49:15 | 2 | ||||||
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OpticalMapping.info Resource Report Resource Website |
OpticalMapping.info (RRID:SCR_017146) | software resource, data or information resource, topical portal, portal | Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data. | platform, tutorial, experimental, design, data, analysis, optical, mapping, structural, labelling, pattern, long, DNA, molecule, fluorescent, signal, capture | Free, Freely available | SCR_017146 | 2026-02-16 09:49:10 | 0 |
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