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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
tRNA Analysis of eXpression Resource Report Resource Website 1+ mentions |
tRNA Analysis of eXpression (RRID:SCR_025486) | tRAX | software application, data processing software, data analysis software, software resource | Software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data. Used for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications. | tRNA-derived small RNAs, mature tRNAs, inference of RNA modifications, high-throughput small RNA sequencing data, | has parent organization: University of California at Santa Cruz; California; USA | NHGRI R01HG006753 | DOI:10.1101/2022.07.02.498565 PMID:26214130 |
Free, Available for download, Freely available, | SCR_025486 | tRNA Analysis of eXpression (tRAX) | 2026-02-15 09:23:53 | 3 | ||||||
|
WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | source code, software toolkit, software resource | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG006123; NIMH MH101825; NIGMS GM007197; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-02-15 09:23:01 | 3 | |||||||||
|
SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | Schmidt Futures ; NHGRI 1RM1HG011543; NSF ; NIMH 1U24MH132628; University of California Office of the President ; QualcommInstitute |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-02-15 09:23:06 | 2 | ||||||||
|
compleasm Resource Report Resource Website 1+ mentions |
compleasm (RRID:SCR_026370) | source code, software resource | Software genome completeness evaluation tool based on miniprot. | genome completeness evaluation, genome, completeness evaluation, | NHGRI R01HG010040; Chan-Zuckerberg Initiative |
PMID:37758247 | Free, Available for download, Freely available | SCR_026370 | 2026-02-15 09:24:10 | 8 | |||||||||
|
RFMix Resource Report Resource Website 1+ mentions |
RFMix (RRID:SCR_027030) | software application, software resource | Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. | Discriminative Modeling, local ancestry and admixture inference, | NLM LM007033; NHGRI 2R01HG003229; NSF |
PMID:23910464 | Restricted | SCR_027030 | 2026-02-15 09:23:29 | 5 | |||||||||
|
PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software toolkit, software resource | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | NHGRI RM1 HG007735; NIGMS R35 GM128636; Howard Hughes Medical Institute ; American Society of Hematology |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-02-15 09:23:51 | 2 | ||||||||
|
HiCDCPlus Resource Report Resource Website 1+ mentions |
HiCDCPlus (RRID:SCR_025317) | software toolkit, software resource | Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP | Hi-C/HiChIP interaction calling, differential analysis, statistical analysis of Hi-C and HiChIP data sets, systematic 3D interaction calls, | NHGRI U01 HG009395; NIDDK U01 DK128852 |
PMID:34099725 | Free, Available for download, Freely available | https://bitbucket.org/leslielab/hicdcplus/src/master/ | SCR_025317 | , HiC-DC+, Hi-C Direct Caller Plus, HiCDCPlus (HiC-DC+) | 2026-02-15 09:23:49 | 1 | |||||||
|
longshot Resource Report Resource Website 1+ mentions |
longshot (RRID:SCR_025318) | source code, software resource | Software variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). Enables accurate variant calling in diploid genomes from single-molecule long read sequencing. Takes as input aligned BAM/CRAM file and outputs phased VCF file with variants and haplotype information. | variant calling, diploid genomes, long error prone reads, single molecule long read sequencing, | NHGRI R01 HG010149 | DOI:10.1038/s41467-019-12493-y | Free, Available for download, Freely available | SCR_025318 | 2026-02-15 09:23:55 | 3 | |||||||||
|
GenVisR Resource Report Resource Website 10+ mentions |
GenVisR (RRID:SCR_027559) | software toolkit, software resource | Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest. | visualizing genomics data, genomics, genomics data, small variants, copy number alterations, data quality, multiple species, | NHGRI K99HG007940; NCI K22CA188163 |
PMID:27288499 | Free, Available for download, Freely available | SCR_027559 | 2026-02-15 09:23:34 | 41 | |||||||||
|
Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, software resource, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root https://bio.tools/cistrome |
SCR_000242 | Galaxy Cistrome | 2026-02-16 09:45:13 | 16 | |||||
|
sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | software application, data processing software, data analysis software, software resource | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth https://bio.tools/sleuth https://bio.tools/sleuth |
SCR_016883 | 2026-02-15 09:21:55 | 24 | ||||||
|
Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | software application, data processing software, data analysis software, software resource | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NHGRI R21 HG006913; NHGRI R01 HG007104; Alfred P. Sloan Research ; NCI T32 CA009337; NHGRI R01 HG005220; NSF BIO-1564917; NSF CCF-1256087; NSF CCF-1053918; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon https://sources.debian.org/src/salmon/ |
SCR_017036 | 2026-02-15 09:21:14 | 357 | ||||||
|
proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | software application, data processing software, data analysis software, software resource | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-02-15 09:21:59 | 1 | |||||||
|
Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | software application, data processing software, data analysis software, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | NIH Office of the Director DP2 OD008540; NHLBI U01 HL130010; NSF PHY-1427654; NHGRI HG006193; Welch Foundation ; Cancer Prevention Research Institute of Texas ; NVIDIA Research Center Award ; IBM University Challenge Award ; Google Research Award ; McNair Medical Institute Scholar Award ; President Early Career Award in Science and Engineering ; NHGRI HG003067; PD Soros Fellowship |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-02-15 09:21:59 | 108 | ||||||||
|
CloVR Resource Report Resource Website 10+ mentions |
CloVR (RRID:SCR_005290) | CloVR | service resource, software resource | A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. | cloud computing, next-generation sequencing |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
Amazon Web Services in Education Research Grants program ; National Human Genome Research Institute ; NHGRI RC2 HG005597-01; NSF 0949201 |
PMID:21878105 | OMICS_01216 | SCR_005290 | CloVR - Automated Sequence Analysis from Your Desktop, Cloud Virtual Resource | 2026-02-15 09:18:56 | 26 | ||||||
|
zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | material resource, biomaterial supply resource | Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NIGMS GM63904; NIDA DA14546; NHGRI HG006431 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-02-15 09:19:37 | 4 | ||||
|
Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, source code, software resource | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | Hanalyzer: A 3R System | 2026-02-15 09:18:01 | 0 | |||||||
|
CHISEL Resource Report Resource Website 1+ mentions |
CHISEL (RRID:SCR_023220) | CHISEL | software application, software resource | Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers. | infer allele and haplotype specific copy numbers, individual cells, low coverage single cell DNA sequencing data, weak allelic signals, weak signals integration, | NHGRI R01HG007069; NCI U24CA211000; NSF CCF 1053753; Chan Zuckerberg Initiative DAF grants ; NCI P30CA072720; O’Brien Family Fund for Health Research ; Wilke Family Fund for Innovation |
DOI:10.1038/s41587-020-0661-6 | Free, Available for download, Freely available | SCR_023220 | Copy-number Haplotype Inference in Single-cell by Evolutionary Links | 2026-02-15 09:23:01 | 2 | |||||||
|
MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-02-16 09:45:19 | 2763 | ||||
|
MouseCyc Resource Report Resource Website 1+ mentions |
MouseCyc (RRID:SCR_001791) | MouseCyc | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. | energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic |
is related to: Mouse Genome Informatics (MGI) is related to: Gene Ontology has parent organization: Jackson Laboratory |
NHGRI HG003622 | PMID:19682380 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10303 | SCR_001791 | MouseCyc database, Mouse Genome Informatics: MouseCyc database | 2026-02-16 09:45:35 | 9 |
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.
