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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Splice AI Resource Report Resource Website 10+ mentions |
Splice AI (RRID:SCR_024532) | data analysis software, data processing software, software resource, software application | Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants. | annotate genetic variants, predicted effect on splicing, identify splice variants, | Free, Available for download, Freely available | https://github.com/Illumina/SpliceAI | SCR_024532 | 2026-08-13 09:30:58 | 44 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, data processing software, software resource, software application | Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, image acquisition, capture high quality images and video, | is listed by: SoftCite | Restricted | SCR_024490 | Teledyne Photometrics Ocular | 2026-08-13 09:31:17 | 4 | |||||||||
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Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | data analysis software, data processing software, software resource, software application | Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. | simulate unmeasured confounding in mediation analysis, mediation analysis, unmeasured confounding, | is listed by: SoftCite | PMID:28724417 | Free, Available for download, Freely available | SCR_024492 | 2026-08-13 09:30:57 | 1 | |||||||||
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Brainways Resource Report Resource Website 1+ mentions |
Brainways (RRID:SCR_024402) | image analysis software, data processing software, software resource, software application | 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 | 2026-08-13 09:31:18 | 1 | ||||||||
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IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | data access protocol, software resource, web service | Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences. | protein structure prediction, protein function prediction, modelling protein structures and functions from amino acid sequences, | is listed by: SoftCite | PMID:25820431 | Free, Freely available | SCR_024523 | 2026-08-13 09:30:58 | 8 | |||||||||
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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 | 2026-08-13 09:30:56 | 2 | |||||||||
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Tn-seq explorer Resource Report Resource Website 1+ mentions |
Tn-seq explorer (RRID:SCR_024387) | data analysis software, data processing software, software resource, software application | Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. | high-throughput sequencing data analysis, transposon mutant libraries, read alignment and gene annotation, identify genes, low counts of transposon insertions genes, | is listed by: Debian | PMID:25938432 | Free, Available for download, Freely available, | https://sources.debian.org/src/tn-seqexplorer/ | SCR_024387 | , Tn-seq Explorer, tn-seqexplorer | 2026-08-13 09:30:56 | 3 | |||||||
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PyWavelets Resource Report Resource Website 10+ mentions |
PyWavelets (RRID:SCR_024421) | data analysis software, data processing software, software resource, software application | Software Python package for wavelet analysis. | Python, wavelet analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024421 | 2026-08-13 09:31:16 | 17 | ||||||||||
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TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_024389) | data analysis software, data processing software, software resource, software application | Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions. | Himar1 TnSeq data analysis, identifying essential genes in individual datasets, comparative analysis between conditions, | is listed by: Debian | PMID:26447887 | Free, Available for download, Freely available, | OMICS_10215 | https://sources.debian.org/src/tnseq-transit/ | SCR_024389 | tnseq-transit | 2026-08-13 09:31:18 | 1 | ||||||
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TREE-PUZZLE Resource Report Resource Website 1+ mentions |
TREE-PUZZLE (RRID:SCR_024382) | data analysis software, data processing software, software resource, software application | Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set. | reconstruct phylogenetic trees, molecular sequence data, maximum likelihood, compute pairwise maximum likelihood distances, conduct statistical tests, data analysis, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_18458 | https://sources.debian.org/src/tree-puzzle/ | https://sources.debian.org/src/tree-ppuzzle/ | SCR_024382 | tree-puzzle | 2026-08-13 09:31:18 | 4 | ||||||
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ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | data analysis software, data processing software, software resource, software application | Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems. | protein identification, protein expression analysis, post translational modification search, | is listed by: SoftCite | Restricted | https://sciex.com/content/dam/SCIEX/pdf/posters/ProteinPilot-Software-Overview.pdf | SCR_024414 | 2026-08-13 09:31:19 | 265 | |||||||||
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sparta Resource Report Resource Website 10+ mentions |
sparta (RRID:SCR_024349) | data analysis software, data processing software, software resource, software application | Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. | analyzing single-end Illumina RNA-seq data, | is listed by: Debian | PMID:26847232 | Free, Available for download, Freely available, | https://sources.debian.org/src/sparta/ | SCR_024349 | SPARTA | 2026-08-13 09:31:15 | 10 | |||||||
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OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | data analysis software, data processing software, software resource, software application | Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL. | OMNISEC instrument control, data acquisition, analysis and reporting, proteins and polymers analysis, | is listed by: SoftCite | Restricted | SCR_024485 | 2026-08-13 09:30:57 | 39 | ||||||||||
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PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | data analysis software, data processing software, software resource, software application | Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously. | probabilistic model, reconstruct species tree and all corresponding gene trees, build gene and species trees, gene families analysis, genomes analysis simultaneously, gene families duplications and losses, | is listed by: SoftCite | PMID:23132911 | Free, Freely available | SCR_024487 | 2026-08-13 09:31:17 | 1 | |||||||||
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Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | data access protocol, software resource, web service | Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma. | survival analysis, assess correlation between expression of genes and survival, tumor samples, | is listed by: SoftCite | PMID:34309564 | Free, Freely available | http://kmplot.com/analysis/index.php?p=service&cancer=custom_plot | SCR_024521 | Kaplan-Meier Plotter, KM Plotter | 2026-08-13 09:31:17 | 6 | |||||||
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ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | data acquisition software, data processing software, software resource, software application | Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras. | image acquisition, Jenoptik ProgRes microscope cameras, Jenoptik, | is listed by: SoftCite | PMID:34520656 | Free, Available for download, Freely available | SCR_024489 | Jenoptic ProgRes Capture Pro | 2026-08-13 09:30:57 | 12 | ||||||||
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MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | data access protocol, software resource, web service | Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library. | large scale protein structure similarity searching, searching similar protein structures, aligning input structure with whole PDB library, | is listed by: SoftCite | PMID:31870277 | Free, Freely available | SCR_024522 | 2026-08-13 09:31:20 | 1 | |||||||||
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National Research Council Resource Report Resource Website 1+ mentions |
National Research Council (RRID:SCR_000446) | data or information resource, organization portal, funding resource, portal | Private, non-profit institution dedicated to utilizing knowledge in science, engineering, technology and health to improve government decision making and public policy as well as increase public education and understanding. The council collects, analyzes and shares information and knowledge through activities such as consensus studies, meetings and workshops, and program and research management. | research, public, policy, nonprofit, education, government, engineering, science, technology, health | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00486 | http://sites.nationalacademies.org/nrc/index.htm | SCR_000446 | NRC | 2026-08-13 09:26:10 | 1 | ||||||||
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Partnership for Interdisciplinary Studies of Coastal Oceans Resource Report Resource Website 1+ mentions |
Partnership for Interdisciplinary Studies of Coastal Oceans (RRID:SCR_024637) | PISCO | organization portal, consortium, data or information resource, portal | Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy. | coastal ocean research, California Current Large Marine Ecosystem, management and policy, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.6085 | SCR_024637 | Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) | 2026-08-13 09:31:22 | 2 | |||||||
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GQuery Resource Report Resource Website 100+ mentions |
GQuery (RRID:SCR_001455) | Entrez | data or information resource, organization portal, database, portal | Search engine for the National Library of Medicine and the National Institutes of Health. It contains databases such as PubMed, EST, and BioSystems. | search engine, national library of medicine, nih, national institutes of health | has parent organization: NCBI | Free, Freely Available | nif-0000-08510 | SCR_001455 | NCBI Entrez, Entrez - The Life Sciences Search Engine | 2026-08-13 09:26:24 | 143 |
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