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.
https://github.com/itojal/hot_scan
A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.
Proper citation: hot scan (RRID:SCR_002840) Copy
https://github.com/PacificBiosciences/SMRT-Analysis/
Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.
Proper citation: SMRT-Analysis (RRID:SCR_002942) Copy
http://compbio.cs.toronto.edu/CNVer/
A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.
Proper citation: CNVer (RRID:SCR_010820) Copy
http://www.popgen.dk/software/index.php/Relate
Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.
Proper citation: Relate (RRID:SCR_010794) Copy
http://compbio.cs.toronto.edu/modil/
Software for a novel method for finding medium sized indels from high throughput sequencing datasets.
Proper citation: MoDIL (RRID:SCR_010764) Copy
http://pgrc.ipk-gatersleben.de/misa/
Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.
Proper citation: MISA (RRID:SCR_010765) Copy
http://www.phenosystems.com/www/index.php/products/gensearchngs
An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.
Proper citation: GensearchNGS (RRID:SCR_010802) Copy
http://www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI/
A software tool that identifies homozygous regions using deep sequence data.
Proper citation: HomSI (RRID:SCR_010771) Copy
http://contra-cnv.sourceforge.net/
A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
Proper citation: CONTRA (RRID:SCR_010814) Copy
https://code.google.com/p/breseq/
A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes.
Proper citation: breseq (RRID:SCR_010810) Copy
http://www.broadinstitute.org/cancer/cga/mutsig
Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
Proper citation: MutSig (RRID:SCR_010779) Copy
http://svdetect.sourceforge.net/Site/Home.html
Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.
Proper citation: SVDetect (RRID:SCR_010812) Copy
Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.
Proper citation: ALLPATHS-LG (RRID:SCR_010742) Copy
http://soap.genomics.org.cn/soapdenovo.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAPdenovo (RRID:SCR_010752) Copy
https://www.hgsc.bcm.edu/content/atlas2
A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data.
Proper citation: Atlas2 (RRID:SCR_010756) Copy
http://berry.engin.umich.edu/oligoarray2_1/
A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.
Proper citation: OligoArray (RRID:SCR_010961) Copy
http://www.cbrc.kaust.edu.sa/hmcan/
A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data.
Proper citation: HMCan (RRID:SCR_010858) Copy
http://furlonglab.embl.de/methods/tools/coco
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression.
Proper citation: CoCo (RRID:SCR_010947) Copy
http://liulab.dfci.harvard.edu/NPS/
A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
Proper citation: NPS (RRID:SCR_010890) Copy
http://linus.nci.nih.gov/BRB-ArrayTools.html
An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BRB-ArrayTools (RRID:SCR_010938) Copy
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:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
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 sources that were queried against in your search that you can investigate further.
Here are the categories present within RRID that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
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.
