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.bioconductor.org/packages/release/bioc/html/ggbio.html
An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
Proper citation: ggbio (RRID:SCR_003313) Copy
http://shendurelab.github.io/MIPGEN/
Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline.
Proper citation: MIPgen (RRID:SCR_003325) Copy
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
Research informatics and analytics platform for the IMI OncoTrack consortium.
Proper citation: eTRIKS (RRID:SCR_003765) Copy
http://genome.sph.umich.edu/wiki/RAREMETAL
A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.
Proper citation: RAREMETAL (RRID:SCR_003573) Copy
http://code.google.com/p/perm/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.
Proper citation: PerM (RRID:SCR_004223) Copy
http://code.google.com/p/rna-star/
Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.
Proper citation: STAR (RRID:SCR_004463) Copy
http://kwanlab.bio.cuhk.edu.hk/BSRD/
A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets.
Proper citation: BSRD (RRID:SCR_004249) Copy
http://iubio.bio.indiana.edu/webapps/SeWeR/
Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C.
Proper citation: SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) Copy
http://bioinfo.au.tsinghua.edu.cn/software/TAGS/
Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TAGS (RRID:SCR_004294) 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
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://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://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://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://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
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
