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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | atlas, reference atlas, data or information resource | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-07-26 09:07:09 | 3 | |||||||||
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Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | software application, software resource, data processing software | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Croatian Science Foundation ; Croatian Academy of Sciences and Arts ; A*STAR ; Singapore |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-07-26 09:07:03 | 149 | ||||||
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LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | software application, software resource, data processing software | Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies. | Chromosome, scale, scaffolding, de novo, genome, assembly, chromatin, Hi-C, data, clustering, contig | NHGRI HG006283; National Science Foundation ; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-07-26 09:07:06 | 62 | ||||||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | software application, software resource, software toolkit, data processing software | 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 |
European Structural and Investment Fund ; European Regional Development Fund ; Belgian Walloon Government ; European Research Council ; Swiss State Secretariat for Education ; Research and Innovation ; German Research Foundation ; Swiss National Science Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Wellcome Trust ; Emory Universitys Research Council ; Swedish Research Council |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-07-26 09:07:07 | 33 | |||||||
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Hierarchical Data Modeling Framework Resource Report Resource Website 1+ mentions |
Hierarchical Data Modeling Framework (RRID:SCR_021303) | HDMF | software application, software resource, software toolkit, data processing software | Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data. | Hierarchical data, data models, reading data, writing data, unified data format, different storage backends, Python object, data, data standards |
is used by: PyNWB is related to: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Documentation Utilities is related to: HDMF Common Schema |
DOI:10.1109/BigData47090.2019.9005648 | Free, Available for download, Freely available | SCR_021303 | 2026-07-26 09:07:42 | 1 | ||||||||
|
FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | software application, software resource, data processing software | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; NIAID R21 AI115014; Welch Foundation ; NSF Graduate Research Fellowship DGE 0940902; NDSEG Fellowship |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-07-26 09:07:12 | 5 | |||||
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viral_seq Resource Report Resource Website 1+ mentions |
viral_seq (RRID:SCR_018515) | software application, software resource, data processing software | Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis. | Processing viral data, next generation sequencing data, viral data, sequencing, HIV drug resistance analysis, Primer ID sequencing, data | Free, Available for download, Freely available | https://github.com/ViralSeq/viral_seq | SCR_018515 | 2026-07-26 09:07:15 | 2 | ||||||||||
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EphysExtraction Resource Report Resource Website 1+ mentions |
EphysExtraction (RRID:SCR_018193) | software application, software resource, data processing software | Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features. | electrophysiological parameter, extract parameter, neuron parameter, voltage trace, data | Free, Available for download, Freely available | SCR_018193 | 2026-07-26 09:07:12 | 2 | |||||||||||
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GeneSyntenyPipeline Resource Report Resource Website |
GeneSyntenyPipeline (RRID:SCR_018198) | software application, software resource, data processing software | Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome. | Genome, synteny, plot, JCVI, gene pair, data | Free, Available for download, Freely available | SCR_018198 | 2026-07-26 09:07:13 | 0 | |||||||||||
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | software application, software resource, data processing software | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891, https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html | SCR_018527 | 2026-07-26 09:07:18 | 8 | |||||||||
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Predomics Resource Report Resource Website 1+ mentions |
Predomics (RRID:SCR_017415) | software application, software resource, source code | Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data. | Metagenomic, data, discover, predictive, signature, unprecedented, interpretability, supervised, learning, ternary, coefficient | EU-FP7 HEALTH-F4-2012-305312; Assistance Publique-Hôpitaux de Paris Contrat d’interface chercheurs 2015-2018; French National Agency |
DOI:10.1101/409144 | Free, Available for download, Freely available | SCR_017415 | 2026-07-26 09:06:59 | 1 | |||||||||
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Allen Brain Atlas expression map of Cre and other drivers Resource Report Resource Website 1+ mentions |
Allen Brain Atlas expression map of Cre and other drivers (RRID:SCR_017510) | atlas, data or information resource | Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice. | Data, image, transgene, expression, Cre, brain, map, mice | has parent organization: Allen Brain Atlas | Free, Freely available | SCR_017510 | Allen Brain Atlas Data Portal Transgenic Characterization | 2026-07-26 09:07:07 | 8 | |||||||||
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Cross Validation Resource Report Resource Website |
Cross Validation (RRID:SCR_000702) | training service resource, 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 | 2026-07-26 09:02:53 | 0 | ||||||||||
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Allen Mouse Spinal Cord Atlas Resource Report Resource Website 10+ mentions |
Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) | Mouse Spinal Cord Atlas | atlas, database, data or information resource | Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments. | gene, expression, adult, diseased, injury, juvenile, models, mouse, postnatal, RNA, hybridization, spinal, cord, molecular, neuroanatomy, data |
has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Free, Freely available | nif-0000-00510 | http://mousespinal.brain-map.org/ | SCR_007418 | 2026-07-26 09:04:27 | 29 | |||||||
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Allen Mouse Brain Connectivity Atlas Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Connectivity Atlas (RRID:SCR_008848) | ABA Mouse Connectivity | atlas, spatially referenced dataset, data or information resource | Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses. | brain, connectivity, atlas, neural, projection, mutant, mouse, strain, image, histology, neuroimaging, data |
is used by: NIF Data Federation is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science | Free for academic use, Non-commercial, Acknowledgement required, Commercial use requires permission | nlx_146253 | http://connectivity.brain-map.org/static/brainexplorer | SCR_008848 | Allen Brain Atlas Connectivity Study, Allen Brain Mouse Connectivity, Allen Mouse Connectivity Atlas, Allen Brain Atlas Mouse Connectivity | 2026-07-26 09:04:41 | 186 | |||||
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Child Language Data Exchange System (CHILDES) Resource Report Resource Website 10+ mentions |
Child Language Data Exchange System (CHILDES) (RRID:SCR_003241) | CHILDES | service resource, database, software resource, storage service resource, data repository, data or information resource | Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats. | Child, language, conversation, interaction, data, psychology, survey, transcript |
is recommended by: National Library of Medicine has parent organization: Carnegie Mellon University; Pennsylvania; USA works with: TalkBank |
NICHD R01 HD23998; NICHD R01 HD051698 |
PMID:2380278 | Free, Freely available | nif-0000-00624, r3d100010887 | https://doi.org/10.17616/R3M31S | http://childes.psy.cmu.edu | SCR_003241 | Child Language Data Exchange System | 2026-07-27 09:31:42 | 46 | |||
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Digital Access to Scholarship at Harvard Resource Report Resource Website |
Digital Access to Scholarship at Harvard (RRID:SCR_004122) | DASH | service resource, database, storage service resource, data repository, data or information resource | Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH. | scholarship, image, audio clip, video resource, manuscript, data | has parent organization: Harvard University; Cambridge; United States | nlx_158606 | SCR_004122 | 2026-07-27 09:31:56 | 0 | |||||||||
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Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility Resource Report Resource Website |
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) | service resource, analysis service resource, access service resource, core facility, production service resource | Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations. | affymetrix, array, PCPGM, gene, expression, data, analysis, service |
is listed by: Eagle I has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156324 | http://www.partners.org/researchcores/trash/bioinformatics_HPCGG.html | SCR_000882 | PCPGM, bioinformatics, The Partners HealthCare Center for Personalized Genetic Medicine | 2026-07-27 09:31:04 | 0 | |||||||
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Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | sequence analysis software, data analysis software, software resource, software application, data processing software | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | 2026-07-27 09:31:07 | 0 | |||||||||
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Waxholm Space Resource Report Resource Website 10+ mentions |
Waxholm Space (RRID:SCR_001592) | WHS, WSA, WSS | atlas, narrative resource, standard specification, waxholm atlas, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files. | mouse WHS atlas, neuroanatomy, mapping, atlas, digital, brain, reference, registration, neuroanatomical, data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Waxholm Space is related to: Duke University; North Carolina; USA is related to: PMOD Software is related to: ITK-SNAP has parent organization: International Neuroinformatics Coordinating Facility has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
PMID:20600960 PMID:21304938 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009594, nlx_153838, nlx_155839 | http://software.incf.org/software/waxholm-space/home, http://www.nitrc.org/projects/incf_waxholm-sp | SCR_001592 | Waxholm Space Atlas, Waxholm Space, Waxholm Standard Space, Mouse WHS atlas | 2026-07-27 09:31:16 | 16 |
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