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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-03 05:00:18 | 34 | ||||||||
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ATACseqMappingPipeline Resource Report Resource Website 1+ mentions |
ATACseqMappingPipeline (RRID:SCR_017558) | data processing software, software application, software resource | Software tool as pipeline to map ATAC-seq data to large genome, for example, for wheat. It splits large genome files into parts and do mapping and then finally merge them. | Map, ATAC-seq, data, genome, large, merge | Free, Freely available | SCR_017558 | 2026-09-03 04:59:57 | 2 | |||||||||||
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ROSE Resource Report Resource Website 50+ mentions |
ROSE (RRID:SCR_017390) | ROSE | data processing software, software application, software resource | To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers . | Stitched, enhancer, separate, super, sequencing, data, file, identified, previously, constituent |
uses: SAMTOOLS uses: Python Programming Language |
Free, Freely available | SCR_017390 | Rank Ordering of Super Enhancers, RANK ORDERING OF SUPER-ENHANCERS | 2026-09-03 04:59:56 | 72 | ||||||||
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Lung Genome Browser Resource Report Resource Website 1+ mentions |
Lung Genome Browser (RRID:SCR_019255) | data or information resource, portal, project portal | Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum. | Genome data, epigenome data, human lung, lung diseases, data, COVID-19 |
is related to: University of California at San Diego; California; USA is related to: LungMap |
human lung diseases | DOI:10.7554/eLife.62522 | Free, Freely available | SCR_019255 | 2026-09-03 05:00:25 | 5 | ||||||||
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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 | 2026-09-03 05:00:01 | 2 | |||||||
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GlyGen Resource Report Resource Website 10+ mentions |
GlyGen (RRID:SCR_023438) | data or information resource, portal, project portal | Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression. | Gly-glycobiology Gen-information, glycobiology, glycans molecular properties, glycans biophysical properties, glycans functional properties properties, glycans, genes, proteins, lipids, pathways and ontologies, data, mutation and expression data, carbohydrate and glycoconjugate related data, | NIGMS 1U01GM125267; NIGMS R24 GM146616 |
PMID:31616925 PMID:32324859 |
Free, Freely available | SCR_023438 | GlyGen Portal | 2026-09-03 05:00:35 | 20 | ||||||||
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PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | data analysis software, data processing software, sequence analysis software, software application, software resource | R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. | chip seq, bayes, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20528864 | Free, Available for download, Freely available | OMICS_00455 | SCR_001093 | Probabilistic inference of ChIP-seq | 2026-09-03 04:57:49 | 3 | |||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NIGMS RC2 GM092519; NIH ; NIMH ; NINDS ; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; Wellcome Trust Strategic Award 095931 |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, SCR_018407, nif-0000-30467 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-09-03 04:57:53 | 29025 | ||||
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Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) Resource Report Resource Website 50+ mentions |
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) | AMP T2D, T2DKP | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease. | type 2 diabetes, diabetes, knowledge, portal, database, repository, type II, diabetic, genetic, data, analysis, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Consortia-pedia is listed by: NIDDK Information Network (dkNET) is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus is related to: Type 1 Diabetes Knowledge Portal is related to: Common Metabolic Diseases Knowledge Portal has parent organization: Foundation for the National Institutes of Health has parent organization: Accelerating Medicines Partnership |
Type 2 diabetes, Diabetes | Broad Institute ; Fundacion Carlos Slim ; NIDDK ; NIH ; University of Michigan |
Free, Freely available | SCR_014533, nlx_157976 | http://www.nih.gov/science/amp/type2diabetes.htm | SCR_003743 | , AMP Diabetes, AMP, T2D, AMP-T2D, Type 2 Diabetes Knowledge Portal, Accelerating Medicines Partnership Type 2 Diabetes, Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, The AMP-T2D Knowledge Portal, AMP T2D, AMP Type 2 Diabetes | 2026-09-03 04:57:59 | 83 | ||||
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BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | data access protocol, data or information resource, portal, project portal, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Breast Cancer Campaign Tissue Bank ; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory ; NSF NRF 2013M3A6A4043695; Sandra Ibarra Foundation for Cancer ; Spanish Government ; U.S. Department of Energy ; Wellcome Trust |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-09-03 04:57:53 | 295 | ||||||
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Phantom Camera Control Resource Report Resource Website 1+ mentions |
Phantom Camera Control (RRID:SCR_021080) | PCC | data analysis software, data processing software, software application, software resource | Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems. | Phantom, Phantom camera, image, data, processing, raw files, convert files | Free, Available for download, Freely available | SCR_021080 | 2026-09-03 04:57:23 | 1 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) | SBP MDI Bioinformatics and Data Management Facility, SBP Medical Discovery Institute Bioinformatics and Data Management Facility, SBP MDI Bioinformatics and Data Management Facility | access service resource, computational hosting, core facility, group, service resource, software resource, training core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician. | data, management, database, bioinformatic, network, connectivity, statistics, analysis, biostatistics, pipeline, software | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014868 | SBP, , Data Management Facility, MDI, Medical Discovery Institute, Sanford Burnham Prebys, Bioinformatics | 2026-09-03 04:52:47 | 0 | |||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canada Research Chairs Program ; Canadian Institutes for Health Research ; Genome Alberta ; Genome Canada ; McGill University ; Natural Sciences and Engineering Research Council of Canada |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-09-03 04:53:28 | 13689 | |||||
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Nextstrain Resource Report Resource Website 100+ mentions |
Nextstrain (RRID:SCR_018223) | data or information resource, data set, portal, project portal | Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools. | Pathogen genome data, data, analytic tool, visualization tool, epidemiology, outbreak response |
is listed by: Data and Computational Resources to Address COVID-19 is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation works with: Global Initiative on Sharing All Influenza Data |
COVID-19 | Free, Freely available | https://nextstrain.org/ncov/global | SCR_018223 | nextstrain.org | 2026-09-03 04:54:55 | 342 | |||||||
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Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | data analysis software, data processing software, software application, software resource | Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas. | Data analysis, data processing, Allen Brain Atlas, data, brain |
is related to: Allen Brain Atlas is organization facet of: BICCN |
Free, Freely available | SCR_018192 | https://allensdk.readthedocs.io/en/latest/ | SCR_018183 | 2026-09-03 04:54:53 | 35 | |||||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | data access protocol, software resource, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-09-03 04:54:45 | 169 | |||||
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IMGT Repertoire Resource Report Resource Website 10+ mentions |
IMGT Repertoire (RRID:SCR_018220) | data or information resource | Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system. | LIGM data, immunoglobulins, T cell receptor, histocompatibility, protein, immune system, data | is related to: IMGT - the international ImMunoGeneTics information system | Free, Freely available | SCR_018220 | IMGT Repertoire (MH), Repertoire (IG and TR), IMGT Repertoire (RPI), ImMunoGeneTics Repertoire | 2026-09-03 04:54:47 | 13 | |||||||||
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Velocyto Resource Report Resource Website 100+ mentions |
Velocyto (RRID:SCR_018167) | data analysis software, data processing software, software application, software resource | Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R. | Expression dynamic, single cell RNAseq data, data, RNAseq, RNA velocity, mRNA, RNAseq dataset, estimation RNA velocity | Free, Available for download, Freely available | https://github.com/velocyto-team/velocyto.py, https://github.com/velocyto-team/velocyto.R | SCR_018167 | velocyto.py, velocyto, velocyto.R | 2026-09-03 04:54:52 | 152 | |||||||||
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astroML Resource Report Resource Website |
astroML (RRID:SCR_018138) | data analysis software, data or information resource, data processing software, data set, data visualization software, software application, software resource, software toolkit | Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics. | Machine learning, statistics, data mining, data, astronomy, astrophysics, data analysis | DOI:10.1109/CIDU.2012.6382200 | Free, Available for download, Freely available | https://github.com/astroML/astroML/blob/master/doc/index.rst | SCR_018138 | 2026-09-03 04:54:57 | 0 | |||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | alignment software, data processing software, image analysis software, software application, software resource | Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets. | Sequence, snap file, single nucleus, ATACseq dataset, data | is used by: scATAC Pipeline | Free, Available for download, Freely available | SCR_018097 | Single Nucleus Accessibility Profile Tools, Single nucleus accessibility profile Tools | 2026-09-03 04:54:56 | 16 |
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