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.
http://www.ch.embnet.org/software/BOX_form.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. This server takes a multiple-alignment file in either GCG''s MSF-format or Clustals ALN-format. Sponsors: This resource was supported by the Swiss EMBnet Node Server. Keywords: Server, Multiple-alignment,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BOXSHADE 3.21 (RRID:SCR_007165) Copy
http://202.97.205.78/epidiff/QDMRTutorial.jsp
Software that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.
Proper citation: QDMR (RRID:SCR_007162) Copy
http://users.utu.fi/mijopi/Pripper/
A tool that can be used to predict caspase cleavage sites from human protein sequences.
Proper citation: Pripper (RRID:SCR_007129) Copy
http://cran.r-project.org/web/packages/evora/
R package for quantifying variation in DNA methylation as a cancer biomarker.
Proper citation: EVORA (RRID:SCR_007329) Copy
http://seurat.r-forge.r-project.org/
Software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data. Visual analytics for the integrated analysis of microarray data.
Proper citation: SEURAT (RRID:SCR_007322) Copy
https://code.google.com/p/peakrots/
Bioinformatics analysis software tool for optimized ChIP-seq peak detection written in R.
Proper citation: peakrots (RRID:SCR_007453) Copy
https://github.com/steinmann/peakzilla
An algorithm to identify transcription factor binding sites from ChIP-seq data.
Proper citation: Peakzilla (RRID:SCR_007471) Copy
Software for identifying haplogroups from low coverage sequence data.
Proper citation: YHap (RRID:SCR_007951) Copy
https://code.google.com/p/ampliconnoise/
A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.
Proper citation: AmpliconNoise (RRID:SCR_007814) Copy
http://web1.sph.emory.edu/users/hwu30/polyaPeak.html
An R package for ranking ChIP-seq peaks with shape information.
Proper citation: polyaPeak (RRID:SCR_007687) Copy
http://www.ensembl.org/info/docs/tools/vep/index.html
Data analysis service to predict the functional consequences of known and unknown variants.
Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy
A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.
Proper citation: Anno-J (RRID:SCR_008192) Copy
https://sites.google.com/site/dadadenoiser/
Infers both the sample genotypes and error parameters that produced a metagenome data set.
Proper citation: DADA (RRID:SCR_008205) Copy
Software package that contains a collection of statistical tools for analysing RNA-seq expression data.
Proper citation: MMSEQ (RRID:SCR_008184) Copy
A cloud platform for next-generation sequencing analysis.
Proper citation: Seven Bridges Genomics (RRID:SCR_008308) Copy
http://epicenter.immunbio.mpg.de/services/chromos/
Combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect.
Proper citation: ChroMoS (RRID:SCR_008320) Copy
http://www.bioconductor.org/packages/release/bioc/html/factDesign.html
Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.
Proper citation: factDesign (RRID:SCR_001330) Copy
http://sourceforge.net/projects/ngsrich/
Software for target enrichment performance for next-generation sequencing.
Proper citation: NGSrich (RRID:SCR_001333) Copy
http://www.bioconductor.org/packages/release/bioc/html/pickgene.html
Software for adaptive Gene Picking for Microarray Expression Data Analysis.
Proper citation: pickgene (RRID:SCR_001331) Copy
https://www.bioconductor.org/packages//2.10/bioc/html/oneChannelGUI.html
Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.
Proper citation: oneChannelGUI (RRID:SCR_001325) 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.
