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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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WinRHIZO Resource Report Resource Website 10+ mentions |
WinRHIZO (RRID:SCR_017120) | data processing software, image analysis software, software application, software resource | Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots. | image, analysis, root, measurement, plant, morphology, topology, color, Regent Instruments Inc. | Available for purchase | SCR_017120 | 2026-09-12 01:01:05 | 16 | |||||||||||
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qMRLab Resource Report Resource Website |
qMRLab (RRID:SCR_016256) | data processing software, image analysis software, software application, software resource | Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models. | mr, image, analysis, simulation, optimize, protocol | Canadian Institute of Health Research (CIHR) ; Fonds de Recherche du Québec ‐ Nature et Technologies FRQNT 2015‐PR‐182754; Natural Sciences and Engineering Research Council of Canada (NSERC) ; Quebec Bio‐Imaging Network QBIN 8436‐0501 |
Open source, Free, Available for download | SCR_016256 | qMTLab, qMR Lab | 2026-09-12 01:01:04 | 0 | |||||||||
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HMS LINCS Center Resource Report Resource Website 10+ mentions |
HMS LINCS Center (RRID:SCR_016370) | HMS LINCS | data or information resource, organization portal, portal | Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation. | LINCS, Program, library, network, cell, signature, analysis, drugs, human, research |
is related to: HMS LINCS Database has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U54 HL127365 | PMID:29199020 | SCR_016370 | LINCS Center, Harvard Medical School LINCS Center, Harvard Medical School LINCS, Harvard Medical School (HMS) LINCS Center | 2026-09-12 01:01:04 | 15 | |||||||
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Cancer Imaging Phenomics Toolkit Resource Report Resource Website 10+ mentions |
Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) | CaPTk | data processing software, image analysis software, software application, software resource | Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome. | analysis, radiographic, cancer, image, quantitative, analytics | is related to: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | Cancer | NCI U24 CA189523 | PMID:29340286 | Free, Available for download, Freely available | https://github.com/CBICA/CaPTk/ | SCR_017323 | Cancer Imaging Phenomics Toolkit | 2026-09-12 01:01:05 | 11 | ||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | data processing software, software application, software resource, software toolkit | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
Belgian Walloon Government ; Emory Universitys Research Council ; European Regional Development Fund ; European Research Council ; European Structural and Investment Fund ; German Research Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Swedish Research Council ; Swiss National Science Foundation ; Swiss State Secretariat for Education ; Research and Innovation ; Wellcome Trust |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-09-12 01:01:06 | 37 | |||||||
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Stereo Investigator - Cleared Tissue Edition Resource Report Resource Website |
Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) | data processing software, image analysis software, software application, software resource | Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses. | Stereology, cleared, tissue, intact, speciment, imaged, confocal, microscopy, analysis, MBF Bioscience | Restricted | SCR_017668 | 2026-09-12 01:01:06 | 0 | |||||||||||
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Argus Resource Report Resource Website 1+ mentions |
Argus (RRID:SCR_021585) | data or information resource, portal, project portal, software resource | Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior. | Analysis, quantification, socially interacting zebrafish, OpenBehavior |
is listed by: OpenBehavior is listed by: SoftCite is related to: Argus |
DOI:10.3758/s13428-018-1083-y | Free, Freely available | SCR_021619 | SCR_021585 | 2026-09-12 01:01:10 | 1 | ||||||||
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gFACs Resource Report Resource Website 1+ mentions |
gFACs (RRID:SCR_022017) | data processing software, software application, software resource | Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis. | filtering, analysis, conversion, unify genome annotations, alignment and gene prediction frameworks, | National Science Foundation Plant Genome Research Program of the United States 1444573 | DOI:10.1016/j.gpb.2019.04.002 | Free, Available for download, Freely available | SCR_022017 | 2026-09-12 01:01:10 | 5 | |||||||||
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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 lists: Active Commutator |
Public | SCR_015938 | 2026-09-12 01:02:53 | 5 | |||||||||
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FLIMfit Resource Report Resource Website 1+ mentions |
FLIMfit (RRID:SCR_016298) | software application, software resource, software toolkit | Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine | United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1; United Kingdom Technology Strategy Board Technology Award CHBT/007/00030; Wellcome Trust WT 095931/Z/11/Z |
PMID:23940626 DOI:10.1371/journal.pone.0070687 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/flimfit/FLIMfit | SCR_016298 | 2026-09-12 01:02:53 | 6 | ||||||||
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sleipner Resource Report Resource Website 1+ mentions |
sleipner (RRID:SCR_018143) | software resource, software toolkit | Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm. | Longitudinal data, analysis, cross sectional data, pattern oriented analysis, | has parent organization: Stockholm University; Stockholm; Sweden | Restricted | SCR_018143 | SLEIPNER, Sleipner, SLEIPNER 2.1 | 2026-09-12 01:02:55 | 2 | |||||||||
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meta Resource Report Resource Website 50+ mentions |
meta (RRID:SCR_019055) | software resource, software toolkit | Software general R package providing standard methods for meta analysis. | Meta analysis, standard methods, meta in R, analysis, statistics |
is listed by: CRAN is related to: dmetar has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
DOI:10.1007/978-3-319-21416-0 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/meta/meta.pdf | SCR_019055 | meta in R | 2026-09-12 01:02:56 | 74 | |||||||
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CellChat Resource Report Resource Website 500+ mentions |
CellChat (RRID:SCR_021946) | software resource, software toolkit | Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. | inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data | Howard Hughes Medical Institute ; LEO Foundation ; NIGMS R01 GM123731; NIH P30 AR07504; NIH U01 AR073159; NSF DMS1763272; Pew Charitable Trust ; Simons Foundation ; UC Irvine |
PMID:33597522 | Free, Available for download, Freely available | http://www.cellchat.org/ | SCR_021946 | 2026-09-12 01:02:59 | 753 | ||||||||
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VisIt Resource Report Resource Website |
VisIt (RRID:SCR_024370) | software application, software resource | Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations. | generate visualizations, animation, analysis, save resulting images and animations for presentations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/visit/ | SCR_024370 | visit | 2026-09-12 01:03:08 | 0 | ||||||||
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Biocode Commons Resource Report Resource Website |
Biocode Commons (RRID:SCR_024553) | data or information resource, portal, topical portal | Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO. | Biological Collections Ontology, Biological Collections Ontology development, genomic observations, collection, analysis, publication, standards community, |
is listed by: DataCite is listed by: University of California; California; USA has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.7286 | SCR_024553 | 2026-09-12 01:00:48 | 0 | |||||||||
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DPARSF Resource Report Resource Website 500+ mentions |
DPARSF (RRID:SCR_002372) | DPARSF | data processing software, software application, software resource, software toolkit | A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely. | magnetic resonance, fmri, resting-state fmri, matlab, analysis, brain |
is used by: DPABI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: RFMRI.ORG |
PMID:20577591 | GNU General Public License | nlx_155735 | http://www.nitrc.org/projects/dparsf | SCR_002372 | Data Processing Assistant for Resting-State fMRI | 2026-09-12 01:00:53 | 696 | |||||
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RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database Resource Report Resource Website |
RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database (RRID:SCR_000086) | RNA STRAND | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A scientific community-crowdsourced database containing the RNA secondary structures of known types and organisms. It is meant to provide a simple and powerful way to analyze, search and update a shared repository of information. | database, rna, analysis, scientific community, resource | has parent organization: University of British Columbia; British Columbia; Canada | PMID:18700982 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03415 | SCR_000086 | RNA secondary STRucture and statistical ANalysis Database | 2026-09-12 01:01:18 | 0 | ||||||
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Sumatra Resource Report Resource Website 10+ mentions |
Sumatra (RRID:SCR_001381) | electronic laboratory notebook, software application, software resource | A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt. | simulation, analysis, python, numerical simulation, manage, track |
uses: Python Programming Language is listed by: INCF Software Center has parent organization: NeuralEnsemble |
Free, Freely Available | nlx_152549 | SCR_001381 | Sumatra: automated tracking of scientific computations | 2026-09-12 01:01:22 | 27 | ||||||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software application, software resource | An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomics |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Principe Felipe Research Centre; Valencia; Spain |
MCyT GEN 2001 - 4885-C05-03; eTumour Project FP6-2002-LIFESCIHEALTH 503094 |
PMID:16081474 | Free for academic use | OMICS_01475, nlx_149335 | SCR_005828 | Blast2GO (B2G) | 2026-09-12 01:02:34 | 8620 | |||||
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ALEA Resource Report Resource Website 50+ mentions |
ALEA (RRID:SCR_006417) | ALEA | software resource, software toolkit | A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype. | allele, epigenomics, analysis, chip-seq, rna-seq, allelic variation, next-generation sequencing |
is listed by: OMICtools has parent organization: BC Cancer Agency |
PMID:24371156 | Academic Free License | OMICS_02193 | SCR_006417 | 2026-09-12 01:02:36 | 95 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
