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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MedBlast Resource Report Resource Website 1+ mentions |
MedBlast (RRID:SCR_008202) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs. | gene, article, biological, data, genome, genomic, homolog, literature, medline interfaces, mining, molecular, protein, sequence, specie | National Natural Science Foundation of China 39990600-03; Knowledge Innovation Program of the Chinese Academy of Sciences KSCX2-2-07; Knowledge Innovation Program of the Chinese Academy of Sciences KJCX1-08 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21253 | SCR_008202 | MedBlast | 2026-02-14 02:01:37 | 1 | ||||||||
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PBmice Resource Report Resource Website 1+ mentions |
PBmice (RRID:SCR_006978) | PBmice | data repository, storage service resource, data or information resource, source code, service resource, software resource, database | Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement. | c57bl/6j, insertional mutation, mutagenesis, piggybac, transposon, insert, mutation | has parent organization: Fudan University; Shanghai; China | Program for New Century Excellent Talents in University ; Chinese Key Projects for Basic Research 2006CB806700; Chinese Key Projects for Basic Research 2005CB321905; Chinese Key Projects for Basic Research 2002CB512801; Hi-tech Research and Development Project 2007AA022012; National Natural Science Foundation of China 60473124; Shanghai Pujiang Program 05PJ14024 |
PMID:17932058 | nlx_97993 | http://www.scbit.org/PBmice/, http://www.idmshanghai.cn/PBmice/ | SCR_006978 | PiggyBac Mutagenesis Information CEnter, PBmice: PiggyBac Mutagenesis Information CEnter | 2026-02-14 02:01:16 | 1 | |||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | data analysis service, production service resource, service resource, analysis service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-02-14 02:05:58 | 386 | ||||
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Database of Arabidopsis Transcription Factors Resource Report Resource Website 10+ mentions |
Database of Arabidopsis Transcription Factors (RRID:SCR_007101) | DATF | data or information resource, database | Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference. | gene, alignment, arabidopsis, binding, clone, dna, domain, locus, phylogenetic tree, transcription, chromosome, transcription factor, blast, family, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
State Key Laboratory of Protein and Plant Gene Research ; National Natural Science Foundation of China 31470330; China 863 Programs 2006AA02Z334; China Postdoctoral Science Foundation Grant 2014M560017 |
PMID:15731212 | Free | nif-0000-21112, OMICS_00551, biotools:datf | https://bio.tools/datf | SCR_007101 | 2026-02-14 02:06:35 | 36 | |||||
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RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/ http://www.rnalocate.org/ |
SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-02-14 02:04:55 | 12 | ||||||
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IPEV Resource Report Resource Website 1+ mentions |
IPEV (RRID:SCR_023702) | data analysis software, software resource, data processing software, software application | Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences. | Prokaryotic and Eukaryotic virus derived sequences, identify sequences, virome, eukaryotic viral sequences, prokaryotic viral sequences, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
DOI:10.1101/2023.05.28.541705 | Free, Available for download, Freely available | SCR_023702 | Identification of Prokaryotic and Eukaryotic Virus | 2026-02-14 02:04:59 | 1 | ||||||||
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TAM Resource Report Resource Website 1+ mentions |
TAM (RRID:SCR_023800) | data access protocol, software resource, web service | Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis. | miRNA set enrichment analysis, functional and disease annotations testing, miRNAs, overrepresentation analysis, | National Natural Science Foundation of China ; Fundamental Research Funds for Central Universities of China ; Natural Science Foundation of Hebei Province ; Doctoral Fund of Ministry of Education of China |
PMID:29878154 PMID:20696049 |
Free, Freely available | SCR_023800 | TAM 2.0 | 2026-02-14 02:05:09 | 2 | ||||||||
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miRBaseConverter Resource Report Resource Website 1+ mentions |
miRBaseConverter (RRID:SCR_023873) | data analysis software, software resource, data processing software, software application | Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends. | converting and retrieving miRNAs information, miRNAs information, different miRBase versions, miRNA Name, miRNA Accession, miRNA Sequence, miRNA Version, miRNA History, miRNA Family, miRNA | Australian Research Council Discovery Project ; National Health and Medical Research council ; Presidential Foundation of Hefei Institutes of Physical Science ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; Applied Basic Research Foundation of Science and Technology of Yunnan Province ; Shanghai Key Laboratory of Intelligent Information Processing China |
PMID:30598108 | Free, Available for download, Freely available | https://github.com/taoshengxu/miRBaseConverter | SCR_023873 | 2026-02-14 02:05:01 | 3 | ||||||||
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PopLDdecay Resource Report Resource Website 100+ mentions |
PopLDdecay (RRID:SCR_022509) | data analysis software, software resource, data processing software, software application | Software tool for linkage disequilibrium decay analysis based on variant call format files. | linkage disequilibrium decay analysis, variant call format, VCF) files | National Natural Science Foundation of China ; China Postdoctoral Science Foundation |
PMID:30321304 | Free, Available for download, Freely available | SCR_022509 | 2026-02-14 02:04:39 | 117 | |||||||||
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PharmMapper Resource Report Resource Website 50+ mentions |
PharmMapper (RRID:SCR_022604) | data access protocol, software resource, web service | Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database. | potential drug target identification, given probe small molecules, identify potential target candidates, binding targets unidentified, pharmacophore mapping approach, drug target identification, target pharmacophore database | National Natural Science Foundation of China ; Shanghai Committee of Science and Technology ; Major National Scientific and Technological Project of China |
PMID:20430828 PMID:28472422 |
Free, Freely available | SCR_022604 | PharmMapper 2017 | 2026-02-14 02:04:40 | 97 | ||||||||
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SC2diseases Resource Report Resource Website 1+ mentions |
SC2diseases (RRID:SCR_019093) | analysis service resource, data or information resource, production service resource, service resource, database | Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases. | Human disease, single cell transcriptome, data, manually curated data, biomarker | National Natural Science Foundation of China | PMID:33010177 | Free, Freely available | SCR_019093 | 2026-02-14 02:03:45 | 5 | |||||||||
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HPEPDOCK Server Resource Report Resource Website 10+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-02-14 02:03:21 | 46 | ||||||
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SOAPBarcode Resource Report Resource Website 100+ mentions |
SOAPBarcode (RRID:SCR_015776) | sequencing analysis software | Software for metabarcoding of DNA. SOAPBarcode takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms and can characterize the biodiversity of large volumes of eukaryote samples. | metabarcoding, metabarcode, bgi, soap, ngs, next generation sequencing, eukaryote | National High-tech Research and Development Project (863) of China 2012AA021601; Yunnan Province 20080A001; Chinese Academy of Sciences 0902281081; Chinese Academy of Sciences KSCX2-YW-Z-1027; National Natural Science Foundation of China 31170498; Ministry of Science and Technology of China 2012FY110800; University of East Anglia |
Free, Available for download | SCR_015776 | metabarcoding | 2026-02-14 02:02:52 | 193 | |||||||||
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CLEAR Resource Report Resource Website 10+ mentions |
CLEAR (RRID:SCR_021663) | data analysis software, software resource, data processing software, software application | Software tool as computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq. CIRCexplorer3-CLEAR is CLEAR pipeline for direct comparison of circular and linear RNA expression. | Strategic Priority Research Program of Chinese Academy of Sciences ; National Natural Science Foundation of China ; Howard Hughes Medical Institute International Program |
PMID:31904419 DOI:10.1101/668657 |
Free, Available for download, Freely available | SCR_021663 | CLEAR/circExplorer3, Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq, CIRCexplorer3-CLEAR | 2026-02-14 02:04:40 | 15 | |||||||||
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Human Potential Tumor Associated Antigen database Resource Report Resource Website 1+ mentions |
Human Potential Tumor Associated Antigen database (RRID:SCR_002938) | data or information resource, database | To accelerate the process of tumor antigen discovery, we generated a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with pTAAs identified by insilico computing. 3518 potential targets have been included in the database, which is freely available to academic users. It successfully screened out 41 of 82 known Cancer-Testis antigens, 6 of 18 differentiation antigen, 2 of 2 oncofetal antigen, and 7 of 12 FDA approved cancer markers that have Gene ID, therefore will provide a good platform for identification of cancer target genes. This database utilizes expression data from various expression platforms, including carefully chosen publicly available microarray expression data, GEO SAGE data, Unigene expression data. In addition, other relevant databases required for TAA discovery such as CGAP, CCDS, gene ontology database etc, were also incorporated. In order to integrate different expression platforms together, various strategies and algorithms have been developed. Known tumor antigens are gathered from literature and serve as training sets. A total tumor specificity penalty was computed from positive clue penalty for differential expression in human cancers, the corresponding differential ratio, and normal tissue restriction penalty for each gene. We hope this database will help with the process of cancer immunome identification, thus help with improving the diagnosis and treatment of human carcinomas. | cancer, tumor, tumor-associated antigen | has parent organization: Chinese Academy of Sciences; Beijing; China | National 863 program in China 2001AA215411; National Natural Science Foundation of China 30531160045; National Natural Science Foundation of China 30570393; Ludwig Institute for Cancer Research KSP 003 |
PMID:16381942 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02987 | http://www.hptaa.org | SCR_002938 | HPtaa Database | 2026-02-14 02:06:12 | 1 | |||||
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shinyCircoss Resource Report Resource Website 1+ mentions |
shinyCircoss (RRID:SCR_022367) | software resource, software application | Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively. | Circos plot, interactive creation |
uses: Shiny uses: R Project for Statistical Computing is related to: RCircos is related to: RStudio is related to: CRAN |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; National Program for Support of Top-notch Young Professionals ; Fundamental Research Funds for the Central Universities |
PMID:29186362 | Free, Available for download, Freely available | https://github.com/YaoLab-Bioinfo/shinyCircos | SCR_022367 | 2026-02-14 02:07:35 | 2 | |||||||
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Resting State Hemodynamic Response Function Retrieval and Deconvolution Resource Report Resource Website 1+ mentions |
Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) | rsHRF | software resource, software toolkit | Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images. | hemodynamic response function, HRF estimation and deconvolution, resting state BOLD signal, GIfTI images, NIfTI images, brain | National Natural Science Foundation of China ; Fund for Scientific Research-Flanders ; European Union Horizon 2020 Framework Programme |
PMID:34560269 | Free, Available for download, Freely available | https://github.com/compneuro-da/rsHRF | SCR_023663 | 2026-02-14 02:07:37 | 3 | |||||||
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lnc2cancer Resource Report Resource Website 10+ mentions |
lnc2cancer (RRID:SCR_023781) | data or information resource, database | Manually curated database of experimentally supported lncRNAs associated with various human cancers. Cancer long non coding RNA database. Lnc2Cancer 3.0 is updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data. | Manually curated database, experimentally supported lncRNAs, human cancer, cancer long non coding RNA, lncRNA/circRNA cancer, | National High Technology Research and Development Program of China ; National Natural Science Foundation of China ; Postdoctoral Science Foundation of China ; Postdoctoral Foundation of Heilongjiang Province ; National Key R and D Program of China ; Heilongjiang Touyan Innovation Team Program ; Heilongjiang Provincial Natural Science Foundation |
PMID:26481356 PMID:33219685 |
Free, Freely available | SCR_023781 | lnc2Cancer 3.0 | 2026-02-14 02:06:27 | 17 | ||||||||
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Beijing: Eyes Open Eyes Closed Study Resource Report Resource Website |
Beijing: Eyes Open Eyes Closed Study (RRID:SCR_001507) | Beijing EOEC | data or information resource, data set | Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed. | early adult human, resting state, fmri, diffusion tensor imaging, resting state fmri, eyes open, eyes closed, neuroimaging, mprage, image collection, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China (863) 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_152810 | SCR_001507 | Beijing Eyes Open Eyes Closed Study, Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Eyes Open Eyes Closed Sample, Eyes Open Eyes Closed Sample, BNU Eyes Open Eyes Closed Sample | 2026-02-14 02:07:45 | 0 | |||||
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Group Information Guided ICA Resource Report Resource Website |
Group Information Guided ICA (RRID:SCR_009491) | GIG-ICA | software resource, software toolkit | Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too. | computational neuroscience, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
Hundred Talent Program of the Chinese Academy of Sciences ; National Basic Research Program of China 973 Program ; National Natural Science Foundation of China 91132707; National Natural Science Foundation of China 30970770 |
PMID:23194820 | Available for download | nlx_155639 | SCR_009491 | 2026-02-14 02:07:20 | 0 |
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