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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OLINDA/EXM Resource Report Resource Website 10+ mentions |
OLINDA/EXM (RRID:SCR_026835) | software application, software resource | Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models. | Calculate radiation doses, evaluate mean absorbed doses to organs and tumors, radionuclide images, clinical trials, | PMID:15937315 PMID:36780284 |
Restricted | SCR_026835 | , Organ Level INternal Dose Assessment/EXponential Modeling, OLINDA/EXM 2, Hermes Medical Solutions OLINDA/EXM | 2026-08-09 09:09:20 | 12 | |||||||||
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READ Resource Report Resource Website 10+ mentions |
READ (RRID:SCR_026958) | software application, software resource | Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals. | infer family relationships, degraded samples, infer degree of relationship, | European Research Council ; Swedish Research Council ; Uppsala Multidisciplinary Center for Advanced Computational Science |
PMID:29684051 | Free, Freely available | SCR_026958 | Relationship Estimation from Ancient DNA | 2026-08-09 09:09:21 | 24 | ||||||||
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Dotmatics ELN and Data Discovery Platform Resource Report Resource Website 1+ mentions |
Dotmatics ELN and Data Discovery Platform (RRID:SCR_027029) | software application, software resource | Software for scientific research and development. ELN captures and manages experimental data, while Data Discovery Platform enables users to explore, analyze, and visualize that data to gain insights. | capture and manage experimental data, explore data, analyze data, visualize data, | Restricted | SCR_027029 | Dotmatics Electronic Lab Notebook and Data Discovery Platform | 2026-08-09 09:09:22 | 2 | ||||||||||
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Concordance Probability Estimates Resource Report Resource Website |
Concordance Probability Estimates (RRID:SCR_027140) | CPE | software toolkit, software resource | Software R package used in survival analysis that evaluates predictive accuracy of survival model. Measures how well model can distinguish between pairs of individuals with different survival times. Calculates proportion of all pairs of individuals whose predicted survival times are correctly ordered. | survival analysis, evaluates predictive accuracy of survival model, predicted survival times, correctly ordered, calculates proportion, | SCR_027140 | CPE: Concordance Probability Estimates in Survival Analysis | 2026-08-09 09:09:37 | 0 | ||||||||||
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mvmeta Resource Report Resource Website 1+ mentions |
mvmeta (RRID:SCR_027142) | software toolkit, software resource | Software R package to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression. | fixed and random-effects, multivariate, univariate, meta-analysis, meta-regression, | Free, Available for download, Freely available | SCR_027142 | 2026-08-09 09:09:23 | 2 | |||||||||||
|
mediation Resource Report Resource Website 1+ mentions |
mediation (RRID:SCR_026984) | software toolkit, software resource | Software R package for estimation of causal mediation effects. Allows researchers to conduct sensitivity analysis for certain parametric models. | estimation of causal mediation effects, sensitivity analysis, parametric models, | Free, Available for download, Freely available | SCR_026984 | 2026-08-09 09:09:34 | 8 | |||||||||||
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PermutMatrix Resource Report Resource Website 1+ mentions |
PermutMatrix (RRID:SCR_026979) | software toolkit, software resource | Software package for analysing and visualising data. Graphical environment to arrange gene expression profiles in optimal linear order. | Graphical environment, arrange gene expression profiles, optimal linear order, | PMID:15546938 | Free, Available for download, Freely available | SCR_026979 | 2026-08-09 09:09:35 | 5 | ||||||||||
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Analysis of Operant Self-administration Behaviors with Supervised Machine Learning Resource Report Resource Website |
Analysis of Operant Self-administration Behaviors with Supervised Machine Learning (RRID:SCR_027003) | source code, software resource | Software repository contains protocol for video acquisition and pose estimation analysis using DeepLabCut and Simple Behavioral Analysis. | video acquisition, pose estimation analysis, protocol, | DOI:10.1523/ENEURO.0031-24.2024 | Free, Available for download, Freely available | SCR_027003 | 2026-08-09 09:09:22 | 0 | ||||||||||
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JaBba Resource Report Resource Website 1+ mentions |
JaBba (RRID:SCR_027134) | software application, software resource | Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments). | Builds genome graph, junctions and read depth, infer junction-balanced genome graphs, whole genome sequencing, inferring optimal copy numbers, vertices and edges, DNA segments, bonds between segments, | NCI P01 CA91955; NCI P30 CA015704 |
PMID:33007263 | Free, Available for download, Freely available, | SCR_027134 | Junction Balance Analysis | 2026-08-09 09:09:23 | 1 | ||||||||
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PRISM - Poisson RNA-profile Identification in Scaled Mixtures Resource Report Resource Website 500+ mentions |
PRISM - Poisson RNA-profile Identification in Scaled Mixtures (RRID:SCR_027136) | PRISM | software application, software resource | Software statistical framework that allows simultaneous extraction of tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples. | simultaneous extraction of tumor sample composition, cell type, sample specific whole-transcriptome profile, individual bulk RNA-seq samples, | European Union Horizon 2020 ; Academy of Finland ; Finnish Cancer Association |
PMID:33720334 | Free, Available for download, Freely available | SCR_027136 | Poisson RNA-profile Identification in Scaled Mixtures | 2026-08-09 09:09:39 | 783 | |||||||
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BAMMtools Resource Report Resource Website 10+ mentions |
BAMMtools (RRID:SCR_027137) | software toolkit, software resource | Software R package for analysis and visualization of macroevolutionary dynamics on phylogenetic trees. | macroevolutionary dynamics, phylogenetic trees, analysis and visualization, | US National Science Foundation | DOI:10.1111/2041-210X.12199 | Free, Available for download, Freely available | SCR_027137 | Bayesian Analysis of Macroevolutionary Mixtures tools | 2026-08-09 09:09:23 | 44 | ||||||||
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FTDock Resource Report Resource Website |
FTDock (RRID:SCR_027019) | software application, software resource | Software tool to discrete two molecules onto orthogonal grids and performs global scan of translational and rotational space. | discrete two molecules onto orthogonal grids, global scan of translational and rotational space, | Restricted | SCR_027019 | 2026-08-09 09:09:36 | 0 | |||||||||||
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COBALT Resource Report Resource Website 10+ mentions |
COBALT (RRID:SCR_027132) | software application, software resource | Software tool to determine read depth ratios of supplied tumor and reference genomes. | determine read depth ratios, supplied tumor, reference genomes, | Free, Available for download, Freely available, | SCR_027132 | COunt BAm Lines T | 2026-08-09 09:09:23 | 15 | ||||||||||
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Ethotrack Resource Report Resource Website 1+ mentions |
Ethotrack (RRID:SCR_027105) | software application, software resource | Video analysis software designed for the study of animal behavior. | Video analysis, study of animal behavior, | Restricted | SCR_027105 | 2026-08-09 09:09:38 | 1 | |||||||||||
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MetaMarkers Resource Report Resource Website 1+ mentions |
MetaMarkers (RRID:SCR_027104) | source code, software resource | Software R package to efficiently compute robust markers across single-cell datasets. Robust marker signatures from single-cell data. | compute robust markers, across single-cell datasets, markers, dataset, marker signatures, single-cell data, | is related to: BRAIN Initiative Cell Atlas Network | Free, Available for download, Freely available | SCR_027104 | Gillis lab MetaMarkers | 2026-08-09 09:09:22 | 6 | |||||||||
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CNAqc Resource Report Resource Website |
CNAqc (RRID:SCR_027066) | software toolkit, software resource | Software package to quality control bulk cancer sequencing data. Used to visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. Used to validate copy number segmentations against variant allele frequencies of somatic mutations. Provides automatic copy number calling pipeline. Provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty. | quality control bulk cancer sequencing datavalidate copy number segmentations, variant allele frequencies, somatic mutations, automatic copy number, | Free, Available for download, Freely available | SCR_027066 | 2026-08-09 09:09:36 | 0 | |||||||||||
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babelgene Resource Report Resource Website 1+ mentions |
babelgene (RRID:SCR_027117) | software toolkit, software resource | Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ). | Integrate orthology assertion predictions, convert, gene, orthologs, homologs | Free, Available for download, Freely available | SCR_027117 | 2026-08-09 09:09:36 | 1 | |||||||||||
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UCell Resource Report Resource Website 10+ mentions |
UCell (RRID:SCR_027109) | software toolkit, software resource | Software package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects. | evaluating gene signatures, single-cell datasets, gene set scoring for single-cell data, | PMID:34285779 | Free, Available for download, Freely available | https://github.com/carmonalab/UCell | SCR_027109 | 2026-08-09 09:09:36 | 24 | |||||||||
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DCHG-DTI Resource Report Resource Website |
DCHG-DTI (RRID:SCR_027264) | source code, software resource | Software repository contains the code for paper: Prediction of Drug-Target Interactions Based on Dual-Channel Heterogeneous Graph Neural Networks. | Prediction of Drug-Target Interactions, Dual-Channel Heterogeneous Graph Neural Networks, | Free, Available for download, Freely available | SCR_027264 | 2026-08-09 09:09:24 | 0 | |||||||||||
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flexmix Resource Report Resource Website 1+ mentions |
flexmix (RRID:SCR_027152) | software toolkit, software resource | Software R package for finite mixtures of regression models using EM algorithm. General framework for finite mixture models and latent class regression in R. | finite mixture models, latent class regression, finite mixtures of regression models, | DOI:10.18637/jss.v011.i08 | Free, Available for download, Freely available | SCR_027152 | Flexible Mixture Modeling | 2026-08-09 09:09:40 | 1 |
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