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://bioinf.wehi.edu.au/limma/
Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
Proper citation: LIMMA (RRID:SCR_010943) 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
A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.
Proper citation: nucleR (RRID:SCR_010895) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
Tools for microarray quality control and pre-processing.
Proper citation: ArrayAnalysis.org (RRID:SCR_010932) Copy
http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm
A robust software package for quantitative comparison of ChIP-Seq data sets.
Proper citation: MAnorm (RRID:SCR_010869) Copy
http://software.big.ac.cn/MeRIP-PF.html
A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.
Proper citation: MeRIP-PF (RRID:SCR_010904) Copy
https://code.google.com/p/batmeth/
Improved mapper for bisulfite sequencing reads on DNA methylation.
Proper citation: BatMeth (RRID:SCR_010906) Copy
You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.
Proper citation: QUMA (RRID:SCR_010907) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://cran.r-project.org/web/packages/DIME/index.html
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Proper citation: DIME (RRID:SCR_010874) Copy
http://bio-bwa.sourceforge.net/
Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
Proper citation: BWA (RRID:SCR_010910) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
https://code.google.com/p/ngsplot/
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
Proper citation: ngs.plot (RRID:SCR_011795) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
http://i122server.vu-wien.ac.at/CANGS1.1/
A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Proper citation: CANGS (RRID:SCR_011837) 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 SPARC SAWG Resources search. From here you can search through a compilation of resources used by SPARC SAWG and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that SPARC SAWG 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 SPARC SAWG then you can log in from here to get additional features in SPARC SAWG 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 SPARC SAWG 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 SPARC SAWG 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.
