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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
eALPS Resource Report Resource Website |
eALPS (RRID:SCR_012130) | software resource | Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD). | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24144111 | OMICS_05833 | SCR_012130 | 2026-08-29 11:24:16 | 0 | |||||||||
|
PLEK Resource Report Resource Website 100+ mentions |
PLEK (RRID:SCR_012132) | software resource | An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. | standalone software, roche, pacific biosciences, unix/linux, c, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25239089 | GNU General Public License | biotools:plek, OMICS_05839 | https://bio.tools/plek | SCR_012132 | PLEK: predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme | 2026-08-29 11:24:20 | 134 | ||||||
|
LDx Resource Report Resource Website |
LDx (RRID:SCR_012131) | software resource | A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23152785 | OMICS_05834 | SCR_012131 | 2026-08-29 11:24:13 | 0 | |||||||||
|
PrimerProspector Resource Report Resource Website 10+ mentions |
PrimerProspector (RRID:SCR_012136) | software resource | A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21349862 | OMICS_05884 | SCR_012136 | 2026-08-29 11:24:16 | 26 | |||||||||
|
Musite Resource Report Resource Website 10+ mentions |
Musite (RRID:SCR_012141) | software resource | A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20702892 | OMICS_05941 | SCR_012141 | 2026-08-29 11:24:20 | 13 | |||||||||
|
PhosphoSiteAnalyzer Resource Report Resource Website |
PhosphoSiteAnalyzer (RRID:SCR_012142) | software resource | A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22471441 | Free, Public | biotools:phosphositeanalyzer, OMICS_05951 | https://bio.tools/phosphositeanalyzer | SCR_012142 | 2026-08-29 11:24:16 | 0 | |||||||
|
CNV Workshop Resource Report Resource Website 1+ mentions |
CNV Workshop (RRID:SCR_012635) | CNV Workshop | software resource | Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV). |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00715 | SCR_012635 | 2026-08-29 11:24:19 | 1 | |||||||||
|
Krona Resource Report Resource Website 50+ mentions |
Krona (RRID:SCR_012785) | Krona | software resource | Software that allows hierarchical data to be explored with zoomable pie charts. | bio.tools |
is listed by: bio.tools has parent organization: SourceForge |
PMID:21961884 | OMICS_01498, biotools:krona | https://bio.tools/krona | SCR_012785 | Krona - Hierarchical data browser | 2026-08-29 11:24:22 | 97 | ||||||
|
Acacia Resource Report Resource Website 100+ mentions |
Acacia (RRID:SCR_012896) | Acacia | software resource | Accurate error-correction of amplicon pyrosequences. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
DOI:10.1038/nmeth.1990 | OMICS_01116 | https://sources.debian.org/src/acacia/ | SCR_012896 | 2026-08-29 11:24:35 | 109 | ||||||||
|
IBDLD Resource Report Resource Website 10+ mentions |
IBDLD (RRID:SCR_013043) | IBDLD | software resource | A C++ software program for multipoint IBD estimation based on high density SNP genotype data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21769932 | Free | OMICS_00204 | SCR_013043 | 2026-08-29 11:24:27 | 15 | |||||||
|
SolSNP Resource Report Resource Website 1+ mentions |
SolSNP (RRID:SCR_013045) | SolSNP | software resource | A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. |
is listed by: OMICtools has parent organization: SourceForge |
MIT License | OMICS_00079 | SCR_013045 | 2026-08-29 11:24:36 | 7 | |||||||||
|
HATS Resource Report Resource Website 10+ mentions |
HATS (RRID:SCR_013044) | HATS | software resource | A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00200 | SCR_013044 | Haplotype Amplification in Tumor Sequences | 2026-08-29 11:24:28 | 38 | |||||||||
|
ChIPOTle Peak Finder Resource Report Resource Website |
ChIPOTle Peak Finder (RRID:SCR_012991) | ChIPOTle Peak Finder | software resource | A peak-finding algorithm used to analyze ChIP-chip microarray data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00803 | SCR_012991 | 2026-08-29 11:24:26 | 0 | ||||||||||
|
Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | data analysis software, data processing software, software application, software resource | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | Differential alternative splicing events, splicing events calculation, RNA-Seq data, gene isoform ratio, alternative splicing patterns, patterns detection, patterns analysis, replicate RNA-Seq data |
is listed by: OMICtools is listed by: SourceForge has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA |
Free, Available for download, Freely available | OMICS_01336, SCR_020941 | SCR_013049 | RNAseq MATS, RMATS, rMATS, MATS, RNA MATS | 2026-08-29 11:24:36 | 203 | |||||||
|
Trinity Resource Report Resource Website 10000+ mentions |
Trinity (RRID:SCR_013048) | Trinity | software resource | Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Broad Institute has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1038/nbt.1883 | biotools:trinity, OMICS_01327 | https://bio.tools/trinity, https://sources.debian.org/src/trinityrnaseq/ | SCR_013048 | 2026-08-29 11:24:28 | 10043 | |||||||
|
NGSpeAnalysis Resource Report Resource Website |
NGSpeAnalysis (RRID:SCR_013040) | NGSpeAnalysis | software resource | A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00291 | SCR_013040 | 2026-08-29 11:24:27 | 0 | |||||||||
|
LoFreq Resource Report Resource Website 500+ mentions |
LoFreq (RRID:SCR_013054) | LoFreq | software resource | A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23066108 DOI:10.1093/nar/gks918 |
Free, Freely available | OMICS_00063 | https://sources.debian.org/src/lofreq/ | SCR_013054 | LoFreq - Sensitive variant-calling from sequencing data | 2026-08-29 11:24:27 | 553 | ||||||
|
GENE-counter Resource Report Resource Website 1+ mentions |
GENE-counter (RRID:SCR_013056) | GENE-counter | software resource | A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21998647 | OMICS_01404, biotools:gene-counter | https://bio.tools/gene-counter | SCR_013056 | 2026-08-29 11:24:36 | 7 | |||||||
|
RNA CoMPASS Resource Report Resource Website |
RNA CoMPASS (RRID:SCR_013058) | RNA CoMPASS | software resource | A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01410 | SCR_013058 | 2026-08-29 11:24:27 | 0 | ||||||||||
|
SNPTools Resource Report Resource Website 10+ mentions |
SNPTools (RRID:SCR_013052) | SNPTools | software resource | A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00075 | SCR_013052 | 2026-08-29 11:24:28 | 19 |
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.
