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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Assembly Based ReAligner Resource Report Resource Website 1+ mentions |
Assembly Based ReAligner (RRID:SCR_003277) | ABRA | software resource | Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular). | standalone software, c, c++, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24907369 | Free, Available for download, Freely available | OMICS_04668, biotools:abra | https://bio.tools/abra | SCR_003277 | ABRA - Assembly Based ReAligner | 2026-08-01 12:02:29 | 7 | |||||
|
NormqPCR Resource Report Resource Website 50+ mentions |
NormqPCR (RRID:SCR_003388) | NormqPCR | software resource | Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data. | gene expression, microtitre plate assay, qpcr, reference gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22748112 | Free, Available for download, Freely available | OMICS_02315, biotools:normqpcr | https://bio.tools/normqpcr | SCR_003388 | NormqPCR - Functions for normalisation of RT-qPCR data | 2026-08-01 12:02:20 | 51 | |||||
|
PoPoolation Resource Report Resource Website 100+ mentions |
PoPoolation (RRID:SCR_003495) | PoPoolation | software resource | A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. | population genetics, next generation sequencing, sliding window, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21253599 | Acknowledgement requested | OMICS_04414, biotools:popoolation | https://bio.tools/popoolation | SCR_003495 | 2026-08-01 12:02:13 | 139 | ||||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | Genome Expression Pathway Analysis Tool | 2026-08-01 12:02:15 | 2 | ||||||
|
J-Express Resource Report Resource Website 50+ mentions |
J-Express (RRID:SCR_003609) | J-Express | software resource | Gene expression analysis software using Java. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is parent organization of: Mini Analysis Guide for Microarrays |
PMID:11301307 | Acknowledgement requested | biotools:j-express, OMICS_00767 | https://bio.tools/j-express | SCR_003609 | J-Express: Gene expression analysis software | 2026-08-01 12:02:32 | 86 | |||||
|
AmpliconNoise Resource Report Resource Website 50+ mentions |
AmpliconNoise (RRID:SCR_007814) | AmpliconNoise | software resource | A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
DOI:10.1186/1471-2105-12-38 | biotools:pyronoise, OMICS_01112 | https://bio.tools/pyronoise, https://sources.debian.org/src/anfo/ | SCR_007814 | 2026-08-01 12:03:34 | 90 | |||||||
|
Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia, https://sources.debian.org/src/minia/ | SCR_004986 | 2026-08-01 12:02:43 | 62 | |||||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-08-01 12:02:53 | 1 | ||||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-08-01 12:02:46 | 4 | ||||||
|
ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | Enhanced Read Analysis of Gene Expression | 2026-08-01 12:02:58 | 30 | ||||||
|
RNA-SeQC Resource Report Resource Website 100+ mentions |
RNA-SeQC (RRID:SCR_005120) | RNA-SeQC | software resource | Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data. | java, bam file, html, sequence comparison, rnaseq, rna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:22539670 | Acknowledgement requested, Public | biotools:rna-seqc, OMICS_01234 | https://bio.tools/rna-seqc | SCR_005120 | 2026-08-01 12:02:49 | 203 | ||||||
|
READSCAN Resource Report Resource Website 1+ mentions |
READSCAN (RRID:SCR_005204) | READSCAN | software resource | A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. | pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:23193222 | OMICS_00222, biotools:readscan | https://bio.tools/readscan | SCR_005204 | 2026-08-01 12:02:47 | 5 | |||||||
|
VirusSeq Resource Report Resource Website 10+ mentions |
VirusSeq (RRID:SCR_005206) | VirusSeq | software resource | An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input. | next-generation sequencing, virus, integration site, cancer tissue, genome, rna-seq, whole genome sequencing, fastq, paired-end read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Texas MD Anderson Cancer Center |
Cancer | OMICS_00227, biotools:virusseq | https://bio.tools/virusseq | SCR_005206 | 2026-08-01 12:02:57 | 23 | |||||||
|
MethPipe Resource Report Resource Website 100+ mentions |
MethPipe (RRID:SCR_005168) | MethPipe | software resource | A computational pipeline for analyzing bisulfite sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:24324667 | biotools:methpipe, OMICS_00603 | https://bio.tools/methpipe | SCR_005168 | 2026-08-01 12:02:56 | 103 | |||||||
|
SnpEff Resource Report Resource Website 5000+ mentions |
SnpEff (RRID:SCR_005191) | SnpEff | software resource | Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. | genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: GATK has parent organization: SourceForge has parent organization: Wayne State University; Michigan; USA works with: SnpSift |
Cancer | PMID:22728672 | Free, Freely available | biotools:snpeff, OMICS_00186 | https://bio.tools/snpeff, https://sources.debian.org/src/snpeff/ | SCR_005191 | SnpEff - Genetic variant annotation and effect prediction toolbox | 2026-08-01 12:02:57 | 5186 | ||||
|
SimRare Resource Report Resource Website 1+ mentions |
SimRare (RRID:SCR_005226) | SimRare | software resource | A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner. | statistical genetics, simulation framework, gui, association test, sequencing, rare variant, python, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code has parent organization: Baylor University; Texas; USA |
PMID:22914216 | Acknowledgement requested, GNU General Public License, v3 | OMICS_00257, biotools:simrare | https://bio.tools/simrare | SCR_005226 | SimRare - A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits | 2026-08-01 12:02:57 | 2 | |||||
|
Breakpointer Resource Report Resource Website 1+ mentions |
Breakpointer (RRID:SCR_005254) | Breakpointer | software resource | A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand. | next-generation sequencing, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
GNU General Public License | biotools:breakpointer, OMICS_00308 | https://bio.tools/breakpointer | SCR_005254 | 2026-08-01 12:02:58 | 9 | |||||||
|
G-Mo.R-Se Resource Report Resource Website 1+ mentions |
G-Mo.R-Se (RRID:SCR_005273) | G-Mo.R-Se | software resource | Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models. | bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01259, biotools:g-mo.r-se, biotools:gmorse | https://bio.tools/g-mo.r-se, https://bio.tools/gmorse | SCR_005273 | Gene MOdeling using RNA-Seq, G-Mo.R-Se: Gene MOdeling using RNA-Seq | 2026-08-01 12:02:51 | 1 | |||||||
|
inGAP Resource Report Resource Website 10+ mentions |
inGAP (RRID:SCR_005261) | inGAP | software resource | Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations. | structural variation, genome, next-generation sequence, genome analysis, alignment, single nucleotide polymorphism, insertion, deletion, indel, inversion, translocation, windows, linux, macos/x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Fudan University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_00319, biotools:ingap | https://bio.tools/ingap | SCR_005261 | inGAP-sv, inGAP-sv: structural variation detection and visualization, integrative next-generation genome analysis pipeline | 2026-08-01 12:02:49 | 29 | |||||||
|
PEMer Resource Report Resource Website 1+ mentions |
PEMer (RRID:SCR_005263) | software resource | Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome. | structural variation, genome, next-generation sequencing, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: BreakDB has parent organization: European Molecular Biology Laboratory |
PMID:19236709 | biotools:pemer, OMICS_00320 | https://bio.tools/pemer, https://bio.tools/pemer | SCR_005263 | Paired-End Mapper | 2026-08-01 12:02:51 | 7 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
