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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PROFisis Resource Report Resource Website |
PROFisis (RRID:SCR_024179) | simulation software, software application, software resource | Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures. | identifies interacting residues from sequence alone, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_13706 | https://sources.debian.org/src/profisis/ | SCR_024179 | profisis | 2026-09-05 06:30:29 | 0 | |||||||
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Ambulatory Monitoring: Psychomotor Vigilance Task system Resource Report Resource Website 1+ mentions |
Ambulatory Monitoring: Psychomotor Vigilance Task system (RRID:SCR_024213) | instrument resource | System includes PVT-192 monitor and REACT software. Used for reaction time testing for long-term, large-scale testing of vigilance, effects of sleep deprivation, and drug effects. Used for PVT test wherever measures of performance or sleepiness effects are needed. | Ambulatory Monitoring Inc., reaction time testing, PVT-192 monitor, REACT software, testing of vigilance, effects of sleep deprivation, drug effects, PVT test, sleepiness effects measurement, instrument, equipment | DOI:10.3758/BF03200977 | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024213.pdf | SCR_024213 | , Psychomotor Vigilance Task, PVT-192 Psychomotor Vigilance Task Monitor | 2026-09-05 06:30:29 | 1 | ||||||||
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ProDA Resource Report Resource Website 1+ mentions |
ProDA (RRID:SCR_024171) | alignment software, data processing software, image analysis software, software application, software resource | Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures. | sequence alignment, protein sequences, protein sequences multiple alignment, repeated sequences, shuffled elements, | is listed by: Debian | DOI:10.1093/nar/gkl511 | Free, Available for download, Freely available, | OMICS_21692 | https://sources.debian.org/src/proda/ | SCR_024171 | proda | 2026-09-05 06:30:29 | 1 | ||||||
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Kleborate Resource Report Resource Website 10+ mentions |
Kleborate (RRID:SCR_024051) | data analysis software, data processing software, software application, software resource | Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive. | screen genome assemblies, Klebsiella pneumoniae, Klebsiella pneumoniae species complex, genome assemblies, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kleborate/ | SCR_024051 | KLEBORATE, kleborate | 2026-09-05 06:30:28 | 27 | ||||||||
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VIGRA Resource Report Resource Website 1+ mentions |
VIGRA (RRID:SCR_024100) | , data processing software, image analysis software, image processing software, software application, software library, software resource, software toolkit | Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework. | image processing and analysis library, customizable algorithms and data structures, multi-dimensional image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libvigraimpex/ | SCR_024100 | , The VIGRA Computer Vision Library, Vision with Generic Algorithms, libvigraimpex | 2026-09-05 06:30:29 | 1 | ||||||||
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pynast Resource Report Resource Website 50+ mentions |
pynast (RRID:SCR_024189) | alignment software, data processing software, image analysis software, software application, software resource | Software tool for aligning sequences to template alignment. | aligning sequences to template alignment, | is listed by: Debian | PMID:19914921 | Free, Available for download, Freely available, | OMICS_15419 | https://sources.debian.org/src/pynast/ | SCR_024189 | Python Nearest Alignment Space Termination tool | 2026-09-05 06:30:29 | 65 | ||||||
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sigma-align Resource Report Resource Website 1+ mentions |
sigma-align (RRID:SCR_024337) | alignment software, data processing software, image analysis software, software application, software resource | Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step. | alignment program, non-coding DNA sequence, | is listed by: Debian | PMID:16542424 | Free, Available for download, Freely available, | OMICS_29594 | https://sources.debian.org/src/sigma-align/ | SCR_024337 | Simple greedy multiple alignment | 2026-09-05 06:30:30 | 1 | ||||||
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signalalign Resource Report Resource Website 1+ mentions |
signalalign (RRID:SCR_024339) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments, | Oxford Nanopore Technologies, MinION sequences DNA, align ionic current, reference sequence, trainable hidden Markov model, HMM-HDP models, MinION signal alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/signalalign/ | SCR_024339 | 2026-09-05 06:30:30 | 2 | |||||||||
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scNTImpute Resource Report Resource Website 1+ mentions |
scNTImpute (RRID:SCR_024395) | data analysis software, data processing software, software application, software resource | Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data. | imputation model, scRNA-seq data, identify dropout values, single-cell RNA sequencing data analysis, | Free, Available for download, Freely available, | SCR_024395 | single-cell Neural Topic Imputation | 2026-09-05 06:30:30 | 1 | ||||||||||
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Patristic Resource Report Resource Website 1+ mentions |
Patristic (RRID:SCR_024154) | data analysis software, data processing software, software application, software resource | Software Java program for calculating patristic distances and graphically comparing the components of genetic change. | calculating patristic distances, graphically comparing the components of genetic change, | is listed by: Debian | PMID:16388682 | Free, Available for download, Freely available, | https://sources.debian.org/src/patristic/ | SCR_024154 | patristic | 2026-09-05 06:30:29 | 5 | |||||||
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ChrAccR Resource Report Resource Website 1+ mentions |
ChrAccR (RRID:SCR_024397) | data analysis software, data processing software, software application, software resource | Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets. | analysis chromatin accessibility data, data quality control, identification and characterization of differentially accessible regions, clustering and quantifying transcription factor activities, | Free, Available for download, Freely available | https://greenleaflab.github.io/ChrAccR/ | SCR_024397 | Chromatin Accessibility data in R | 2026-09-05 06:30:30 | 2 | |||||||||
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Efficient and Adaptive Gaussian Smoothing Resource Report Resource Website 1+ mentions |
Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) | EAGS | data analysis software, data processing software, software application, software resource | Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell. | determine neighborhood cells relationship, calculate cell gene expression, high resolved spatial transcriptomics, spatial transcriptome data, data with ultrahigh resolution, | Free, Available for download, Freely available, | SCR_024399 | 2026-09-05 06:30:30 | 1 | ||||||||||
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ScanProsite Resource Report Resource Website 100+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | data access protocol, software resource, web service | Web tool for detecting PROSITE signature matches in protein sequences. | detecting PROSITE signature matches, protein sequences, | is listed by: SoftCite | Swiss National Science Foundation ; Swiss Federal Government |
Free, Freely available | https://www.expasy.org/resources/scanprosite | SCR_024425 | 2026-09-05 06:30:31 | 106 | |||||||
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PlasmidSeeker Resource Report Resource Website 10+ mentions |
PlasmidSeeker (RRID:SCR_024167) | data analysis software, data processing software, software application, software resource | Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads. | k-mer based program, identification of known plasmids, whole genome sequencing reads, | is listed by: Debian | PMID:29629246 | Free, Available for download, Freely available, | OMICS_28371 | https://sources.debian.org/src/plasmidseeker/ | SCR_024167 | plasmidseeker | 2026-09-05 06:30:29 | 17 | ||||||
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recan Resource Report Resource Website |
recan (RRID:SCR_024317) | data analysis software, data processing software, software application, software resource | Software tool as genetic distance plotting for recombination events analysis. | genetic distance plotting, recombination events analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/recan/ | SCR_024317 | 2026-09-05 06:30:30 | 0 | |||||||||
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SoftCite Resource Report Resource Website |
SoftCite (RRID:SCR_024411) | data or information resource, knowledge base, portal, project portal, software resource | Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale. | Gold standard dataset, software mentions, research publications, annotated software mentions, full text academic literature, |
lists: ProteinPilot lists: ROCit lists: survivalROC lists: GIFT lists: PyWavelets lists: pRRophetic lists: GOplot lists: Rgdal lists: riskRegression lists: RNAfold lists: RNALocate lists: pyPCcazip lists: ScanProsite lists: RapGreen lists: ABySS lists: AMBER lists: ANNOVAR lists: ASAP lists: ASPicDB lists: AStalavista lists: ATSAS lists: Alien hunter lists: Adobe Photoshop lists: Affymetrix lists: Augustus lists: Argus lists: Adobe Illustrator lists: ART lists: AutoDock Vina lists: AutoDock lists: ANALYZE lists: BLASTClust lists: arrayQualityMetrics lists: BLASTN lists: BLASTX lists: BLASTP lists: Bowtie lists: Autogrid lists: BRB-ArrayTools lists: BEDTools lists: BWA lists: BioEdit lists: BRASS lists: Bioconductor lists: BioExtract lists: BaCelLo lists: BioMoby lists: Brain Extraction Tool lists: Bowtie 2 lists: BoxPlotR lists: biomaRt lists: BioPerl lists: CANGS lists: CFX Manager lists: CEAS lists: BlobFinder lists: CLC Genomics Workbench lists: BREAKDANCER lists: CASAVA lists: CLC Main Workbench lists: ClustalW lists: Clustal W2 lists: ComBat lists: CCP4 lists: Blender lists: Coot lists: CGView lists: COMSOL Multiphysics lists: CTFFIND lists: CalcuSyn lists: ChIPpeakAnno lists: Chimera lists: CVODE lists: DAVID lists: Cufflinks lists: caret lists: ClueGO lists: Cluster lists: Clocklab lists: DIANA-mirPath lists: Cytoscape lists: EMAN lists: E-Prime lists: DESeq2 lists: Definiens Developer XD lists: Eigensoft lists: EMBOSS lists: Ensembl lists: DIALIGN lists: Design-Expert lists: EndNote lists: CMAP lists: EEGLAB lists: CMap lists: Epi Info lists: FASTA lists: Ensembl Genome Browser lists: Epik lists: FACS lists: FCS Express lists: Flowlogic lists: FSL lists: FLASH lists: FATCAT lists: FastQC lists: G*Power lists: GOLD lists: FGENESH lists: FreeSurfer lists: FlowJo lists: GeneTools lists: Galaxy lists: GATK lists: ELDA lists: GraphPad lists: GRADEpro lists: Fiji lists: Gblocks lists: FigTree lists: GENIE lists: GBrowse lists: Gemma lists: GeneChip Operating Software lists: GeneMapper lists: GeneMarker lists: GenABEL lists: GenePattern lists: GraphPad Prism lists: GenePix Pro lists: Google lists: Genesis lists: Hologic lists: GeneSpring GX lists: GeneVenn lists: HaploReg lists: Google Scholar lists: HALO lists: Gwyddion lists: IMAGIC lists: HKL-2000 lists: Glide lists: Glimmer lists: I-TASSER lists: GenomeStudio lists: IMOD lists: Haploview lists: Hmmer lists: Hydra lists: IUPRED lists: HomeCageScan lists: Geneious lists: IGOR Pro lists: IMPUTE lists: Infernal lists: Image-Pro Plus lists: JASP lists: LSM Image Examiner lists: Imaris lists: Image Pro Plus lists: ImageQuant lists: ImageJ lists: Integrative Genomics Viewer lists: jcvi lists: InterProScan lists: KaleidaGraph lists: Ligprep lists: Heidelberg Eye Explorer lists: JMP lists: Ingenuity Pathways Knowledge Base lists: Leica QWin lists: JCB DataViewer lists: Jalview lists: LigandScout lists: Ingenuity Pathway Analysis lists: LabView lists: Kepler lists: MAFFT lists: Jmol lists: ImageScope lists: MACS lists: Maq lists: MUMmer lists: MATLAB lists: Mimics lists: MACH lists: MCODE lists: Mascot lists: Maestro lists: MSQuant lists: MediaWiki lists: MINC lists: MRIcron lists: MOE lists: ModFit LT lists: LIMMA lists: MassLynx lists: mitopred lists: MrBayes lists: MolProbity lists: MUSCLE lists: MutationAssessor lists: MaxQuant lists: Minitab lists: MODELLER lists: MetaboAnalyst lists: MedCalc lists: Origin lists: MPlus lists: MutationTaster lists: MuTect lists: Multi Gauge lists: NIA Array Analysis lists: NIH Image lists: Phenix lists: MycoBank lists: OpenClinica lists: Nexus lists: OMTools lists: NIS-Elements lists: PAST lists: NVivo lists: PRISM (Stanford database) lists: Metscape lists: PROCHECK lists: oligo lists: OpenEpi lists: Pathway Commons lists: Nanoparticle Tracking Analysis lists: Openlab lists: PLINK lists: PAUP lists: NONMEM lists: PREFAB lists: NetworkX lists: PeptideProphet lists: Primer Designer lists: PhyML lists: PASS lists: PyMOL lists: PSIPRED lists: PROFILER lists: PHYLIP lists: Phobius lists: Prime lists: Phyutility lists: Picard lists: ProteinProphet lists: Phaser lists: ProSAS lists: PostgreSQL lists: Primer-BLAST lists: ProteinLynx Global Server lists: QUANTO lists: Primer Express lists: Primer3Plus lists: ProtTest lists: ProbCons lists: Primer3 lists: Poretools lists: Protein preparation Wizard lists: QmRLFS-finder lists: PicTar lists: RevMan lists: Pipeline Pilot lists: QIIME lists: PRISMA lists: REDCap lists: RAxML lists: Proteome Discoverer lists: Research Randomizer lists: SPARTAN lists: SPSS lists: RNAstructure lists: Refmac lists: QuantPrime lists: Prodigal lists: RepeatModeler lists: Ringo lists: SQLite lists: SAGE lists: Rhinoceros lists: SAMTOOLS lists: SPAdes lists: RepeatMasker lists: SEDFIT lists: STATISTICA lists: RNAhybrid lists: SlideBook lists: STRUCTURE lists: SABmark lists: SPM lists: Stata lists: RStudio lists: SciPy lists: Scion Image lists: Simulink lists: TAGGER lists: TopHat lists: SAM lists: ShortRead lists: SIFT lists: SCAN lists: SignalP lists: Scopus lists: Strelka2 lists: Trans-ABySS lists: Statgraphics Centurion lists: T-Coffee lists: Statistical Analysis System lists: TargetScan lists: UCHIME lists: Sequencher lists: SigmaStat lists: UCSC Genome Browser lists: affy lists: Taverna lists: MBF BioScience: Stereo Investigator lists: Trimmomatic lists: Vmatch lists: WFU PickAtlas lists: SigmaPlot lists: X!Tandem lists: STAR lists: TASSEL lists: SyStat lists: WEBLOGO lists: UCSF Chimera lists: TreeView lists: pheatmap lists: WinWCP lists: microRNA.org lists: glmnet lists: Phenix.refine lists: BASE lists: beadarray lists: RMS lists: lumi lists: Web of Science lists: minfi lists: geNORM lists: WU-BLAST lists: WinBUGS lists: SPP lists: tRNAscan-SE lists: WebPlotDigitizer lists: qBasePLUS lists: Matplotlib lists: TreeBASE lists: pClamp lists: TBLASTN lists: igraph lists: V3D lists: survival lists: miRanda lists: piRNABank lists: topGO lists: NGmerge lists: OMNISEC lists: NOTUNG lists: OpenBUGS lists: Optimization Toolbox lists: ProgRes Capture Pro lists: Ocular lists: Umediation lists: Nano Measurer lists: PHYLDOG lists: VSEARCH lists: WinNonlin lists: WHONET lists: ToposPro lists: Treerecs lists: Agilent Seahorse Wave lists: SimPhy lists: TomoStudio lists: Mutation Assessor lists: Stem lists: SRAMP lists: CRISPResso2 lists: geepack lists: Evalue lists: DAGitty lists: FastMulRFS lists: ggridges lists: gamm4 lists: AutoRT lists: CopyKAT lists: Inference of CRISPR Edits lists: classInt lists: ASTRAL-Pro lists: maftools lists: mitml lists: CMplot lists: MetaPSICOV lists: LaCyTools lists: MADOKA lists: Kaplan Meier Plotter lists: IntFOLD lists: ModFOLD lists: lDDT has parent organization: University of Texas at Austin; Texas; USA |
Sloan Foundation | DOI:10.1002/asi.24454 | Free, Available for download, Freely available | https://github.com/softcite/softcite_dataset_v2, https://zenodo.org/record/7995565 | SCR_024411 | Software Citation | 2026-09-05 06:30:30 | 0 | ||||||
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Lighter Resource Report Resource Website |
Lighter (RRID:SCR_024095) | data analysis software, data processing software, software application, software resource | Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. | kmer-based error correction method, whole genome sequencing data, correct the reads containing sequence errors, | is listed by: Debian | PMID:25398208 | Free, Available for download, Freely available, | https://sources.debian.org/src/lighter/ | SCR_024095 | lighter | 2026-09-05 06:30:29 | 0 | |||||||
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Brainways Resource Report Resource Website 1+ mentions |
Brainways (RRID:SCR_024402) | data processing software, image analysis software, software application, software resource | Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices. | OpenBehavior, slice quantification, register coronal slices, quantify fluorescent markers, slice matching to atlas, registration and analysis of fluorescent markers, coronal brain slices, | is listed by: OpenBehavior | DOI:10.1101/2023.05.25.542252 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/brainways/ | SCR_024402 | 2026-09-05 06:30:30 | 1 | ||||||||
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RiboToolkit Resource Report Resource Website 1+ mentions |
RiboToolkit (RRID:SCR_024406) | data access protocol, software resource, web service | Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. | Ribo-seq data analysis, analysis and annotation of ribosome profiling data, decode mRNA translation at codon resolution, data cleaning and quality evaluation, | NCI R35 CA232115 | PMID:32427338 | Free, Freely available | SCR_024406 | 2026-09-05 06:30:30 | 2 | |||||||||
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ramr Resource Report Resource Website |
ramr (RRID:SCR_024408) | data analysis software, data processing software, software application, software resource | Software R package for detection of low frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. Provides functions to visualize found aberrantly methylated regions, to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms. | rare aberrantly methylated regions, low frequency aberrant methylation events detection, visualize found aberrantly methylated regions, | K.G. Jebsen foundation ; Norwegian Cancer Society ; Norwegian Health Region West ; Norwegian Research Council |
PMID:34383893 | Free, Available for download, Freely available | https://github.com/BBCG/ramr | SCR_024408 | rare aberrantly methylated regions | 2026-09-05 06:30:30 | 0 |
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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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