Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ArCH Resource Report Resource Website 1+ mentions |
ArCH (RRID:SCR_025975) | ArCH | software resource, software toolkit | Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants. | sequencing studies analysis, somatic variant calling, detect low variant allele fraction, clonal hematopoiesjsonsis variants, | American Society of Hematology ; Edward P. Evans Foundation ; NCI K08 CA241318; NCI P30 CA008748 |
PMID:38485690 | Free, Available for download, Freely available, | SCR_025975 | SciCrunch Registry | , ArCH: Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline, Artifact Filtering Clonal Hematopoiesis Variant Calling Pipeline | 2026-10-17 01:38:58 | 1 | |||||||
|
TRUST4 Resource Report Resource Website 10+ mentions |
TRUST4 (RRID:SCR_026162) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length. | analyze TCR and BCR sequences, de novo assembly, unselected RNA sequencing data, fluid and solid tissues, tumors, | NCI U01CA226196; NCI U24CA224316 |
PMID:33986545 | Free, Available for download, Freely available | SCR_026162 | SciCrunch Registry | 2026-10-17 01:37:02 | 12 | |||||||||
|
TNBCtype Resource Report Resource Website 1+ mentions |
TNBCtype (RRID:SCR_026238) | software resource, web application | Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile. | predicting subtype, triple negative breast cancer sample, gene expression profile, | American Cancer Society ; Komen Foundation ; NCI CA009385; NCI CA068485; NCI CA070856; NCI CA105436; NCI CA148375; NCI CA95131 |
PMID:22872785 | Free, Freely available | SCR_026238 | SciCrunch Registry | 2026-10-17 01:39:00 | 4 | |||||||||
|
scVital Resource Report Resource Website 1+ mentions |
scVital (RRID:SCR_026215) | software application, software resource, source code | Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data. | embed scRNA-seq data, species-agnostic latent space, overcome batch effect, identify cell states shared between species, cross-species integration, scRNA-seq data, | NCI K08 CA267072; NCI P30 CA08748; NCI R01 CA290400; NIA R01 AG054720 |
DOI:10.1101/2024.12.20.629285 | Free, Available for download, Freely available | SCR_026215 | SciCrunch Registry | 2026-10-17 01:37:04 | 1 | |||||||||
|
DSigDB Resource Report Resource Website 100+ mentions |
DSigDB (RRID:SCR_026202) | data or information resource, database | Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | SciCrunch Registry | , Drug Signatures Database, drug SIGnatures DataBase | 2026-10-17 01:37:43 | 165 | ||||||||
|
FACETS Resource Report Resource Website 10+ mentions |
FACETS (RRID:SCR_026264) | data analysis software, data processing software, software application, software resource, source code | Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing. | Allele-specific copy number, clonal heterogeneity analysis, estimating genome copy numbers, high throughput DNA sequencing data, Fraction and Copy number Estimate from Tumor/normal Sequencing, | NCI CA124514; NCI CA163251; NCI CA195365; NCI P01 CA129243; NCI P30 CA008748; Susan G. Komen for the Cure |
PMID:27270079 | Free, Available for download, Freely available, | SCR_026264 | SciCrunch Registry | 2026-10-17 01:39:01 | 22 | |||||||||
|
Eastern Cooperative Oncology Group Performance Status Scale Resource Report Resource Website 1+ mentions |
Eastern Cooperative Oncology Group Performance Status Scale (RRID:SCR_026432) | data or information resource, narrative resource, organization portal, portal, standard specification | ECOG Performance Scale describes patient’s level of functioning in terms of their ability to care for themself, daily activity, and physical ability (walking, working, etc.). Standard criteria for measuring how the disease impacts patient’s daily living abilities. Used to assess the functional status of patient. | ECOG-ACRIN Cancer Research Group, patient’s performance status, assess patient functional status, conduct clinical trials, | NCI | Free, Freely available | SCR_026432 | SciCrunch Registry | ECOG Performance Status Scale | 2026-10-17 01:39:03 | 5 | |||||||||
|
MeTPeak Resource Report Resource Website 10+ mentions |
MeTPeak (RRID:SCR_026533) | software resource, software toolkit, source code | Software package for finding the location of m6A sites in MeRIP-seq data. | finding location of m6A sites, MeRIP-seq data | Natural Science Foundation of China ; NCI P30CA54174; NCI U54 CA113001; NIGMS R01 GM113245; NSF |
PMID:27307641 | Free, Available for download, Freely available | SCR_026533 | SciCrunch Registry | 2026-10-17 01:37:12 | 11 | |||||||||
|
HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | software resource, source code, web application | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | SciCrunch Registry | 2026-10-17 01:37:17 | 45 | |||||||||
|
AMICI Resource Report Resource Website |
AMICI (RRID:SCR_026913) | software resource, software toolkit, source code | Software toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification. Used for high-performance sensitivity analysis for large ordinary differential equation models. | high-performance sensitivity analysis, large ordinary differential equation models, | European Unions Horizon 2020 ; Federal Ministry of Education and Research of Germany ; German Research Foundation ; NCI U54 CA225088 |
PMID:33821950 | Free, Available for download, Freely available | SCR_026913 | SciCrunch Registry | Advanced Multilanguage Interface to CVODES and IDAS | 2026-10-17 01:37:27 | 0 | ||||||||
|
OpenTOPAS Resource Report Resource Website 1+ mentions |
OpenTOPAS (RRID:SCR_026927) | software application, software resource, source code | Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit. | Monte Carlo method, particle simulation, simulation of medical applications, ionizing radiation, | NCI R01 CA140735; NCI U24 CA215123 |
PMID:23127075 PMID:32247964 |
Free, Available for download, Freely available | https://opentopas.github.io/ | SCR_026927 | SciCrunch Registry | , TOPAS, TOol for PArticle Simulation | 2026-10-17 01:38:01 | 2 | |||||||
|
apeglm Resource Report Resource Website 1+ mentions |
apeglm (RRID:SCR_026951) | software resource, software toolkit | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NCI P01 CA142538; NHGRI R01 HG009125; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | SciCrunch Registry | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-10-17 01:38:02 | 2 | ||||||||
|
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 | SciCrunch Registry | Junction Balance Analysis | 2026-10-17 01:37:35 | 1 | ||||||||
|
Palantir Resource Report Resource Website 1+ mentions |
Palantir (RRID:SCR_027194) | algorithm resource, software resource, source code | Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state. | Trajectory, align cells along differentiation trajectories, | NCI P30 CA008748; NCI R01CA164729; NICHD DP1-HD084071 |
PMID:30899105 | Free, Available for download, Freely available | SCR_027194 | SciCrunch Registry | 2026-10-17 01:37:35 | 5 | |||||||||
|
SeSAMe Resource Report Resource Website 10+ mentions |
SeSAMe (RRID:SCR_027388) | SeSAMe | software resource, software toolkit | Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. | reducing artifactual detection, DNA methylation, Infinium BeadChips, genomic deletions, | Michelle Lunn Hope Foundation ; NCI R01 CA170550; NCI U24 CA143882; NCI U24 CA210969; Ovarian Cancer Research Fund Grant ; Van Andel Research Institute |
PMID:30085201 | Free, Available for download, Freely available, | SCR_027388 | SciCrunch Registry | SEnsible Step-wise Analysis of DNA MEthylation | 2026-10-17 01:37:43 | 23 | |||||||
|
SYGNAL Resource Report Resource Website 1+ mentions |
SYGNAL (RRID:SCR_023080) | software resource, software toolkit | Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts. | Integrating genomic and transcriptomic measurements, human cohorts, transcriptional regulatory networks, integrate correlative, causal and mechanistic inference, unified framework, infers causal flow of information, mutations to TFs, miRNAs to perturbed gene expression patterns across patients, | American Cancer Society Research Scholar Grant ; NCI U24CA143835; NIGMS P50GM076547; NIGMS R01GM077398; NSF ABI NSF-1262637; NSF DBI-0640950 |
PMID:27426982 | Free, Available for download, Freely available | SCR_023080 | SciCrunch Registry | SYstems Genetic Network AnaLysis | 2026-10-17 01:35:06 | 1 | ||||||||
|
mtradeR Resource Report Resource Website 1+ mentions |
mtradeR (RRID:SCR_022977) | software resource, software toolkit | Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually. | test association between taxa and disease risk, correlated taxa screening, taxa and disease risk | American Lebanese Syrian Associated Charities ; NCI CA21765; NIDDK U24DK097771 |
PMID:36123651 | Free, Available for download, Freely available | SCR_022977 | SciCrunch Registry | Metagenomic TRajectory Analysis with Disease Endpoint and Risk factors | 2026-10-17 01:34:33 | 1 | ||||||||
|
SCRuB Resource Report Resource Website 1+ mentions |
SCRuB (RRID:SCR_023518) | software resource, software toolkit | Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program. | Source tracking, contamination removal, microBiomes, MiSeq decontamination, contamination in microbial studies, | CIFAR Azrieli Global Scholarship ; Columbia University ; NCI R01CA245894; NICHD R01HD106017; Rockefeller University |
PMID:36928429 | Free, Available for download, Freely available | SCR_023518 | SciCrunch Registry | Source-tracking for Contamination Removal in microBiomes, Source tracking for Contamination Removal in microBiomes | 2026-10-17 01:34:36 | 2 | ||||||||
|
bam readcount Resource Report Resource Website 10+ mentions |
bam readcount (RRID:SCR_023653) | software application, software resource | Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads. | BAM file, CRAM file, sequencing data, nucleotide positions, | Edward P. Evans Foundation ; NCI 1U01CA209936; NCI K22CA188163; NCI P01CA101937; NCI R50CA211782; NCI U24CA237719; NHGRI R00 HG007940 |
PMID:34341766 | Free, Available for download, Freely available | SCR_023653 | SciCrunch Registry | bam-readcount | 2026-10-17 01:36:14 | 38 | ||||||||
|
University of Wisconsin-Madison Advanced Genome Editing Laboratory Resource Report Resource Website 10+ mentions |
University of Wisconsin-Madison Advanced Genome Editing Laboratory (RRID:SCR_021070) | AGEL | access service resource, core facility, service resource | Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications. | USEDit, generating genome edited models, mouse, rats, swine, ABRF, ABRF, CRISPR, gene editing, genome editing, lentiCRISPR |
is listed by: ABRF CoreMarketplace has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NCI P30 CA014520 | ABRF_1148 | https://coremarketplace.org/?FacilityID=1148 | SCR_021070 | SciCrunch Registry | University of Wisconsin Madison UW-Genome Editing & Animal Models, UW-Genome Editing & Animal Models, University of Wisconsin Madison Advanced Genome Editing Laboratory, UW Biotechnology Center Advanced Genome Editing Laboratory, Genome Editing and Animal Models Core, University of Wisconsin Madison Genome Editing Core Facility, Transgenic Animal Facility | 2026-10-17 01:37:53 | 14 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
