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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | data or information resource, organization portal, portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-09-19 12:56:05 | 16 | ||||||
|
Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, image analysis software, software application, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-09-19 12:56:05 | 15 | ||||||
|
Porechop Resource Report Resource Website 1000+ mentions |
Porechop (RRID:SCR_016967) | data processing software, software application, software resource | Software tool for finding and removing adapters from Oxford Nanopore reads. | finding, removing, adapter, Oxford Nanopore, read, sequencing, data |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_17306 | https://sources.debian.org/src/porechop/ | SCR_016967 | 2026-09-19 12:56:06 | 1350 | ||||||||
|
PopMedNet Resource Report Resource Website 1+ mentions |
PopMedNet (RRID:SCR_016456) | PopMedNet | data or information resource, portal | Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks. | implement, distribute, health, data, network, research, coordinate, center, governance, | has parent organization: Harvard Medical School; Massachusetts; USA | NIH DRN ; the HHS Assistant Secretary for Planning and Evaluation ; The National Institutes of Health |
PMID:27141522 | Free, Available for download, Freely available | https://github.com/PopMedNet-Team/popmednet | SCR_016456 | Population Medicine Network | 2026-09-19 12:56:05 | 3 | |||||
|
glmmADMB Resource Report Resource Website 1+ mentions |
glmmADMB (RRID:SCR_016859) | data processing software, software application, software resource | Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions. | generalized, linear, mixed, model, ADMB, count, data, Poisson, negative, binominal, distribution |
uses: AD Model Builder is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | http://r-forge.r-project.org/projects/glmmadmb/ | SCR_016859 | glmm AD Model Builder, generalized linear mixed models using AD Model Builder, generalized linear mixed models using ADMB | 2026-09-19 12:56:06 | 3 | ||||||||
|
cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | data processing software, image analysis software, software application, software resource | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-09-19 12:56:05 | 2939 | |||||||||
|
MaRe Resource Report Resource Website 1+ mentions |
MaRe (RRID:SCR_018069) | data processing software, software application, software resource, software toolkit | Software tool to leverage power of Docker and Spark to run and scale your serial tools in MapReduce fashion. | Docker, Spark, run and scale serial tools, data, MapReduce fashion | Free, Available for download, Freely available | SCR_018069 | EasyMapReduce | 2026-09-19 12:56:09 | 3 | ||||||||||
|
Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | data or information resource, portal, project portal | Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility. | Reproducible, data, merging, science, cyberinfrastructure, pathway, tale, capture, code, finding, analysis | NSF 1541450 | DOI:10.1016/j.future.2017.12.029 | Free, Freely available | https://github.com/whole-tale/wt-design-docs//blob/stable/README.rst | SCR_017537 | 2026-09-19 12:56:08 | 1 | ||||||||
|
Clarivate Analytics Resource Report Resource Website 50+ mentions |
Clarivate Analytics (RRID:SCR_017657) | data or information resource, organization portal, portal | Data analytics company that operates a collection of services: Web of Science (EndNote, InCites, Journal Citation Reports, Publons, Kopernio), Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, and ScholarOne. Deliver critical data, information, workflow solutions and deep domain expertise to innovators everywhere. | Data, analytics, Web of Science, Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, ScholarOne. | SCR_017657 | 2026-09-19 12:56:08 | 82 | ||||||||||||
|
Nonhuman Primate Reference Transcriptome Resource Resource Report Resource Website 10+ mentions |
Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) | NHPRTR | data or information resource, portal, project portal | Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. | Nonhuman, primate, reference, transcriptome, deep, sequencing, RNAseq, data, species | NIH | Free, Freely available | SCR_017534 | Nonhuman Primate Reference Transcriptome Resource | 2026-09-19 12:56:08 | 12 | ||||||||
|
DiffuserCam Resource Report Resource Website |
DiffuserCam (RRID:SCR_017466) | data processing software, software application, software resource | Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam. | Processing, code, multiplier, algorithm, recovering, 3D, volume, 2D, raw, data, capture, BRAIN Initiative | is recommended by: BRAIN Initiative | NEI EY027597 | Free, Freely available | SCR_017466 | 2026-09-19 12:56:07 | 0 | |||||||||
|
Compilation of Genetics Resource Databases Resource Report Resource Website 50+ mentions |
Compilation of Genetics Resource Databases (RRID:SCR_017501) | data or information resource, portal | Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse. | Genetic, data, brain, atlas, information, National, Institute, Drug, Abuse, FASEB list | Restricted | SCR_017501 | 2026-09-19 12:56:07 | 61 | |||||||||||
|
Optogenetics Resource at JAX Resource Report Resource Website |
Optogenetics Resource at JAX (RRID:SCR_017508) | data or information resource, portal | Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science. | Data, mouse, line, expressing, protein, activate, inhibit, detect, neuronal, activity, JAX | Free, Freely available | SCR_017508 | 2026-09-19 12:56:08 | 0 | |||||||||||
|
CopyNumber450kCancer Resource Report Resource Website 1+ mentions |
CopyNumber450kCancer (RRID:SCR_017965) | data processing software, software application, software resource | Software R package baseline correction for accurate copy number calling from 450k methylation array. Baseline correction for copy number data from cancer samples. Implements maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct baseline in cancer samples. | Correction, accurate, copy, number, calling, 450k, methylation, array, data, cancer, maximum, density, peak, estimation | has parent organization: Uppsala University; Uppsala; Sweden | Swedish Cancer Society ; Swedish Foundation for Strategic Research ; Swedish Research Council for Science and Technology |
PMID:26553913 | Free, Freely available | SCR_017965 | 2026-09-19 12:56:08 | 3 | ||||||||
|
ProteomeTools Resource Report Resource Website 10+ mentions |
ProteomeTools (RRID:SCR_018535) | data or information resource, portal, project portal | Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research. | Molecular tool, human proteome, proteome, human, peptide, data |
is related to: ProteomicsDB is related to: ProteomeXchange |
Alexander von Humboldt Foundation ; American Recovery and Reinvestment Act ; European Research Council ; German Federal Ministry of Education and Research ; NCRR S10 RR027584; NHGRI RC2 HG005805; NIGMS P50 GM076547; NIGMS R01 GM087221; Swiss National Science Foundation |
PMID:28135259 | Free, Freely available | http://www.proteometools.org | SCR_018535 | 2026-09-19 12:56:10 | 23 | |||||||
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fs-tool Resource Report Resource Website 1+ mentions |
fs-tool (RRID:SCR_018250) | data processing software, software application, software resource | Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes. | calculate fraction of shared peptides, peptides between HLA proteins, HLA alleles, NetMHCpan binding prediction, genotype, data | Free, Available for download, Freely available | SCR_018250 | fraction shared tool | 2026-09-19 12:56:09 | 1 | ||||||||||
|
Data Browser Resource Report Resource Website 10+ mentions |
Data Browser (RRID:SCR_017561) | data or information resource, organization portal, portal | National research resource to provide interactive views of publicly available All of Us Research Program participant data including electronic health record data, biospecimens, surveys, and other measures taken at time of participant enrollment. Data platform will be open to researchers all over world and show data for groups of de-identified participants. Data is updated periodically. | All of Us Research, program, participant, data, surey, physical, measurement, electronic, health, record | SCR_017561 | 2026-09-19 12:56:08 | 30 | ||||||||||||
|
Single Read Paired Read Indel Substitution Minimizer Resource Report Resource Website 1+ mentions |
Single Read Paired Read Indel Substitution Minimizer (RRID:SCR_018023) | SRPRISM | data processing software, software application, software resource | Software tool as single read paired read indel substitution minimizer. | Single read, paired indel, substitution minimizer, next generation sequencing, data, indel | Free, Available for download, Freely available | https://github.com/ncbi/SRPRISM/tree/master/srprism | SCR_018023 | Single Read Paired Read Indel Substitution Minimizer | 2026-09-19 12:56:09 | 3 | ||||||||
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HeuDiConv: a heuristic-centric DICOM converter Resource Report Resource Website 10+ mentions |
HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) | HeuDiConv | data processing software, software application, software resource | Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts. | Flexible, DICOM, converter, organizing, brain, image, data, structured, directory, layout | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | http://www.nitrc.org/projects/heudiconv/ | SCR_017427 | heudiconv, heuristic-centric DICOM converter | 2026-09-19 12:56:07 | 34 | ||||||||
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scATAC Pipeline Resource Report Resource Website 1+ mentions |
scATAC Pipeline (RRID:SCR_018919) | data processing software, software application, software resource | Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics. | Data, data processing, single nuclei, ATAC-seq datasets, paired reads processing, FASTQ file |
uses: SnapTools is used by: BICCN has parent organization: Broad Institute is organization facet of: Terra |
Free, Available to download, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/scATAC, https://app.terra.bio/#workspaces/brain-initiative-bcdc/scATAC | https://github.com/HumanCellAtlas/skylab/tree/master/pipelines/snap-atac | SCR_018919 | single cell ATAC, scATAC | 2026-09-19 12:56:10 | 2 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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