Searching across hundreds of databases
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://owww.molgen.mpg.de/~abt_rop/molecular_cytogenetics/GenomeCAT.html
A software for the analysis and visualization of array CGH data.
Proper citation: CGHPRO (RRID:SCR_010921) Copy
http://cran.r-project.org/web/packages/cghseg/index.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Software R package dedicated to the analysis of CGH profiles using segmentation models.
Proper citation: CGHseg (RRID:SCR_010922) 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
A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.
Proper citation: BASE (RRID:SCR_010937) 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.
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
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://zhanglab.c2b2.columbia.edu/index.php/MCarts
A hidden Markov model (HMM)-based software to predict clusters RNA motif sites.
Proper citation: mCarts (RRID:SCR_010902) 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/bsolana/
An approach for the analysis of two-base encoding bisulfite sequencing data.
Proper citation: B-SOLANA (RRID:SCR_010905) 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://ww2.odu.edu/~nxkim/nextpeak/
A software program to call peaks from ChIP-seq data for transcription factor binding sites.
Proper citation: NEXT-peak (RRID:SCR_010862) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
https://code.google.com/p/bsmap/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS).
Proper citation: RRBSMAP (RRID:SCR_010864) Copy
http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS
An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity.
Proper citation: SIPeS (RRID:SCR_010865) Copy
http://www.math.miami.edu/~vhower/tpic.html
A software for determining DNA/protein binding sites from a ChIP-Seq experiment.
Proper citation: T-PIC (RRID:SCR_010867) Copy
http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPDiff.htm
Provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2).
Proper citation: ChIPDiff Library Comparison (RRID:SCR_010871) 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
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.
