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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | EasyMapReduce | 2026-09-19 12:56:09 | 3 | ||||||||||
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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 | SciCrunch Registry | 2026-09-19 12:56:08 | 1 | ||||||||
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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 | SciCrunch Registry | Nonhuman Primate Reference Transcriptome Resource | 2026-09-19 12:56:08 | 12 | ||||||||
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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 | SciCrunch Registry | 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 | SciCrunch Registry | 2026-09-19 12:56:07 | 61 | |||||||||||
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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 | SciCrunch Registry | 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 | SciCrunch Registry | 2026-09-19 12:56:10 | 23 | |||||||
|
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 | SciCrunch Registry | 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 | SciCrunch Registry | 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 | SciCrunch Registry | Single Read Paired Read Indel Substitution Minimizer | 2026-09-19 12:56:09 | 3 | ||||||||
|
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 | SciCrunch Registry | heudiconv, heuristic-centric DICOM converter | 2026-09-19 12:56:07 | 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 | SciCrunch Registry | 2026-09-19 12:56:08 | 2 | |||||||||||
|
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 | SciCrunch Registry | Rank Ordering of Super Enhancers, RANK ORDERING OF SUPER-ENHANCERS | 2026-09-19 12:56:07 | 72 | ||||||||
|
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 | SciCrunch Registry | 2026-09-19 12:56:11 | 5 | ||||||||
|
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 | SciCrunch Registry | GlyGen Portal | 2026-09-19 12:56:16 | 20 | ||||||||
|
wavethresh Resource Report Resource Website 1+ mentions |
wavethresh (RRID:SCR_024311) | software resource, software toolkit | Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation. | perform 1D, 2D and 3D real and complex valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage, data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-wavethresh/ | SCR_024311 | SciCrunch Registry | 2026-09-19 12:56:23 | 3 | |||||||||
|
PMAP Resource Report Resource Website |
PMAP (RRID:SCR_000740) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers. | proteolytic pathway, proteolysis, database, data | has parent organization: Sanford Burnham Prebys Medical Discovery Institute | PMID:18842634 PMID:16448029 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03318 | SCR_000740 | SciCrunch Registry | 2026-09-19 12:56:28 | 0 | ||||||||
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Cancer Gene Index Resource Report Resource Website 1+ mentions |
Cancer Gene Index (RRID:SCR_001117) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data. | gene, cancer, genetics, pharmacology, disease, database, data |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01575 | SCR_001117 | SciCrunch Registry | 2026-09-19 12:56:29 | 2 | ||||||||
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EPDnew Resource Report Resource Website 10+ mentions |
EPDnew (RRID:SCR_002485) | HT-EPD, EPD | data or information resource, database | EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters. | Promoter collection, eukaryotic promoter, promoter specific high throughput data, species specific data, experimentally validated promoter, promoter, data |
is listed by: OMICtools is related to: Eukaryotic Promoter Database is related to: Eukaryotic Promoter Database has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Government ; Swiss National Science Foundation |
PMID:27899657 PMID:23193273 |
Free, Available for download, Freely available | nif-0000-02806 | https://epd.expasy.org/ | SCR_002485 | SciCrunch Registry | , Eukaryotic Promoter Database, Eukaryotic Promoter Database new | 2026-09-19 12:56:36 | 27 | ||||
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UniGene Resource Report Resource Website 1000+ mentions |
UniGene (RRID:SCR_004405) | UniGene | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters. | colleciton, data, information, organized, view, transcriptome, locus, protein, similarity, gene, expression, |
is used by: Rank Rank Hypergeometric Overlap is listed by: OMICtools is listed by: re3data.org is related to: ProbeMatchDB 2.0 is related to: Bgee: dataBase for Gene Expression Evolution is related to: GeneSpeed- A Database of Unigene Domain Organization has parent organization: NCBI works with: Digital Differential Display (DDD) |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_41571, OMICS_01663, r3d100010774 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene, https://doi.org/10.17616/R35G7T | SCR_004405 | SciCrunch Registry | NCBI UniGene, Organized View of the Transcriptome, UniGene | 2026-09-19 12:56:44 | 1153 |
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