Searching across hundreds of databases

Our searching services are busy right now. Your search will reload in five seconds.

  • Register
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X

Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

No
Yes
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Search

Type in a keyword to search

on page 1 showing 20 out of 24 results

Cite this (AutoAssemblyD, RRID:SCR_001087)

URL: http://sourceforge.net/projects/autoassemblyd/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

  • From Current Category

    BAC

Cite this (BAC, RRID:SCR_001067)

URL: http://www.bioconductor.org/packages/release/bioc/html/BAC.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

  • From Current Category

Cite this (BS Seeker, RRID:SCR_005641)

URL: http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site.

  • From Current Category

    bsseq

Cite this (bsseq, RRID:SCR_001072)

URL: http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R package with tools for analyzing and visualizing bisulfite sequencing data.

  • From Current Category

    CpGassoc

Cite this (CpGassoc, RRID:SCR_000320)

URL: http://cran.r-project.org/web/packages/CpGassoc/index.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A software designed to test the association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The software can perform standard analyses of large datasets without the need to manually input the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. This software also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

  • From Current Category

    CSDeconv

Cite this (CSDeconv, RRID:SCR_000016)

URL: http://crab.rutgers.edu/~dslun/csdeconv/index.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.

  • From Current Category

    Dissect

Cite this (Dissect, RRID:SCR_000058)

URL: http://dissect-trans.sourceforge.net/Home

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

  • From Current Category

    DSGseq

Cite this (DSGseq, RRID:SCR_001104)

URL: http://bioinfo.au.tsinghua.edu.cn/software/DSGseq/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R software program for identifying differentially spliced genes from two groups of RNA-seq samples. It reads the count file and outputs the differences in the relative abundance of the isoforms of each gene in the annotation.

  • From Current Category

    GMATo

Cite this (GMATo, RRID:SCR_000165)

URL: http://sourceforge.net/projects/gmato/files/?source=navbar

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.

  • From Current Category

Cite this (Illuminator, RRID:SCR_001019)

URL: http://dna.leeds.ac.uk/illuminator/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels.

  • From Current Category

    Jmosaics

Cite this (Jmosaics, RRID:SCR_001094)

URL: http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R software that detects enriched regions of ChIP-seq data sets jointly.

  • From Current Category

    Mugsy

Cite this (Mugsy, RRID:SCR_001414)

URL: http://mugsy.sourceforge.net/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.

  • From Current Category

Cite this (Mutation Surveyor, RRID:SCR_001247)

URL: http://www.softgenetics.com/mutationSurveyor.php

Resource Type: Resource, software resource, software application, sequence analysis software, data analysis software, data processing software

Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.

  • From Current Category

    Phred

Cite this (Phred, RRID:SCR_001017)

URL: http://www.codoncode.com/productsservices/phrap.htm#PHRED

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A base calling program for DNA sequence traces.

  • From Current Category

    PICS

Cite this (PICS, RRID:SCR_001093)

URL: http://www.bioconductor.org/packages/2.12/bioc/html/PICS.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.

  • From Current Category

Cite this (R453Plus1Toolbox, RRID:SCR_001105)

URL: http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.

  • From Current Category

    rGADEM

Cite this (rGADEM, RRID:SCR_001091)

URL: http://www.bioconductor.org/packages/2.12/bioc/html/rGADEM.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R package with tools for de novo motif discovery in large-scale genomic sequence data.

  • From Current Category

    RmiR

Cite this (RmiR, RRID:SCR_001069)

URL: http://www.bioconductor.org/packages/release/bioc/html/RmiR.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R package that contains functions to merge microRNA and respective targets using different databases.

  • From Current Category

Cite this (Sequencher, RRID:SCR_001528)

URL: http://genecodes.com/sequencher

Resource Type: Resource, software resource, software application, sequence analysis software, data analysis software, data processing software

Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data.

  • From Current Category

Cite this (ShortFuse, RRID:SCR_001107)

URL: https://bitbucket.org/mckinsel/shortfuse

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.

  • From Current Category

  1. RRID Portal Resources

    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.

  2. Navigation

    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.

  3. Logging in and Registering

    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.

  4. Searching

    Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:

    1. Use quotes around phrases you want to match exactly
    2. You can manually AND and OR terms to change how we search between words
    3. You can add "-" to terms to make sure no results return with that term in them (ex. Cerebellum -CA1)
    4. You can add "+" to terms to require they be in the data
    5. Using autocomplete specifies which branch of our semantics you with to search and can help refine your search
  5. Save Your Search

    You can save any searches you perform for quick access to later from here.

  6. Query Expansion

    We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.

  7. Collections

    If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.

  8. Sources

    Here are the sources that were queried against in your search that you can investigate further.

  9. Categories

    Here are the categories present within RRID that you can filter your data on

  10. Subcategories

    Here are the subcategories present within this category that you can filter your data on

  11. Further Questions

    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.

X