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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | Copy Number Inference From Exome Reads | 2026-02-14 02:02:50 | 195 | ||||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-02-14 02:02:24 | 7 | ||||||||
|
PIA Resource Report Resource Website |
PIA (RRID:SCR_013267) | PIA | software resource | A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00676 | SCR_013267 | 2026-02-14 02:02:28 | 0 | |||||||||
|
Wgsim Resource Report Resource Website 100+ mentions |
Wgsim (RRID:SCR_013269) | Wgsim | software resource | A small tool for simulating sequence reads from a reference genome. | is listed by: OMICtools | OMICS_00260 | SCR_013269 | 2026-02-14 02:02:24 | 161 | ||||||||||
|
SOAPdenovo-Trans Resource Report Resource Website 100+ mentions |
SOAPdenovo-Trans (RRID:SCR_013268) | SOAPdenovo-Trans | software resource | A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01324 | SCR_013268 | 2026-02-14 02:02:51 | 170 | |||||||||
|
BRAT Resource Report Resource Website 50+ mentions |
BRAT (RRID:SCR_013159) | BRAT | software resource | BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer. | is listed by: OMICtools | OMICS_00577 | SCR_013159 | Bisulfite-treated Reads Analysis Tool | 2026-02-14 02:02:46 | 53 | |||||||||
|
CEM Resource Report Resource Website 1+ mentions |
CEM (RRID:SCR_013241) | CEM | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
OMICS_01271, biotools:cem | https://bio.tools/cem | SCR_013241 | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | 2026-02-14 02:02:28 | 1 | |||||||
|
SeqSite Resource Report Resource Website |
SeqSite (RRID:SCR_013243) | SeqSite | software resource | Software for detecting transcription factor binding sites from ChIP-seq data. | is listed by: OMICtools | OMICS_00493 | SCR_013243 | SeqSite: ChIP-Seq Binding Site Identification | 2026-02-14 02:02:23 | 0 | |||||||||
|
Repitools Resource Report Resource Website 10+ mentions |
Repitools (RRID:SCR_013242) | Repitools | software resource | Software tools for the analysis of enrichment-based epigenomic data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00619 | SCR_013242 | 2026-02-14 02:02:50 | 21 | ||||||||||
|
SmashCommunity Resource Report Resource Website 1+ mentions |
SmashCommunity (RRID:SCR_013245) | SmashCommunity | software resource | A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. |
is listed by: OMICtools has parent organization: EMBL - Bork Group |
OMICS_01482 | SCR_013245 | 2026-02-14 02:02:47 | 8 | ||||||||||
|
miRSeqNovel Resource Report Resource Website 1+ mentions |
miRSeqNovel (RRID:SCR_013257) | miRSeqNovel | software resource | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
Free, Public, Non-commercial | OMICS_00381 | SCR_013257 | 2026-02-14 02:02:51 | 2 | |||||||||
|
AutoMap Resource Report Resource Website 50+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | 2026-02-14 02:02:21 | 92 | ||||||||||
|
DynamicProg Resource Report Resource Website |
DynamicProg (RRID:SCR_013217) | DynamicProg | software resource | A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01150 | SCR_013217 | 2026-02-14 02:02:28 | 0 | ||||||||||
|
muliAlignFree Resource Report Resource Website |
muliAlignFree (RRID:SCR_013188) | muliAlignFree | software resource | R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:23990418 | Free | OMICS_00981 | SCR_013188 | muliAlignFree: Multiple Alignment-free Sequence Comparison | 2026-02-14 02:02:22 | 0 | |||||||
|
CancerMutationAnalysis Resource Report Resource Website |
CancerMutationAnalysis (RRID:SCR_013181) | CancerMutationAnalysis | software resource | Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer. |
is listed by: OMICtools has parent organization: Bioconductor |
Cancer | OMICS_00141 | SCR_013181 | 2026-02-14 02:02:50 | 0 | |||||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-02-14 02:02:50 | 37 | ||||||
|
CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-02-14 02:02:28 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-02-14 02:02:22 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-02-14 02:02:28 | 66 | ||||||||||
|
HMMSplicer Resource Report Resource Website 1+ mentions |
HMMSplicer (RRID:SCR_013315) | HMMSplicer | software resource | An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
OMICS_01241 | SCR_013315 | 2026-02-14 02:02:47 | 3 |
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.
