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://home.gwu.edu/~wpeng/Software.htm
A clustering software package for identification of enriched domains from histone modification ChIP-Seq data.
Proper citation: SICER (RRID:SCR_010843) Copy
http://www.netlab.uky.edu/p/bioinfo/MapSplice
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery.
Proper citation: MapSplice (RRID:SCR_010844) Copy
Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.
Proper citation: TargetScan (RRID:SCR_010845) Copy
http://groups.csail.mit.edu/pag/mirnaminer/
A web-based tool used for homologous miRNA gene search in several species. The code is available on request.
Proper citation: miRNAminer (RRID:SCR_010850) Copy
http://sourceforge.net/p/mira-assembler/wiki/Home/
Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.
Proper citation: MIRA (RRID:SCR_010731) Copy
http://www.comp.nus.edu.sg/~bioinfo/peasm/PE_manual.htm
Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized.
Proper citation: PE-Assembler (RRID:SCR_010732) Copy
A quality-value guided de novo short read assembler.
Proper citation: QSRA (RRID:SCR_010733) Copy
http://compbio.med.harvard.edu/Supplements/BMCBioinfo10-2.html
Designed to identify CNVs between two genomes.
Proper citation: rSW-seq (RRID:SCR_010825) Copy
http://www.broadinstitute.org/software/cprg/?q=node/39
An algorithm to identify chromosomal breakpoints using massively parallel next generation sequence data.
Proper citation: SegSeq (RRID:SCR_010826) Copy
Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data.
Proper citation: miRDeep (RRID:SCR_010829) Copy
Offers the researchers an automatic pipeline to predict the disease-association of SAPs.
Proper citation: SAPRED (RRID:SCR_010785) Copy
https://rostlab.org/services/snap/
A method for evaluating effects of single amino acid substitutions on protein function.
Proper citation: SNAP - Effects of Single Amino Acid Substitutions on Protein Function (RRID:SCR_010786) Copy
http://bg.upf.edu/transfic/home
A method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes.
Proper citation: TransFIC (RRID:SCR_010788) Copy
http://seqanswers.com/wiki/JointSLM
Copy number estimation from read depth information.
Proper citation: JointSLM (RRID:SCR_010823) Copy
http://genetics.cs.ucla.edu/eminim/
A software tool for imputation of unobserved genotypes using a set of reference haplotype panel at a higher-density SNP set such as HapMap, and lower-density genotypes of a target individual using such as genotyping arrays.
Proper citation: EMINIM (RRID:SCR_010790) Copy
http://genetics.cs.ucla.edu/harsh/
Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data.
Proper citation: HARSH (RRID:SCR_010792) Copy
http://www.bioinf.jku.at/research/short-IBD/
Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data.
Proper citation: HapFABIA (RRID:SCR_010793) Copy
http://www3a.biotec.or.th/c-mii/
A software tool for plant miRNA and target identification. C-mii pipelines are based on combined steps and criteria from previous studies and also incorporated with several tools such as standalone BLAST and UNAFold and pre-installed databases including miRBase, UniProt, and Rfam. C-mii provides following distinguished features. First, it comes with graphical user interfaces of well-defined pipelines for both miRNA and target identifications with reliable results. Second, it provides a set of filters allowing users to reduce the number of results corresponding to the recently proposed constraints in plant miRNA and target biogenesis. Third, it extends the standard computational steps of miRNA target identification with miRNA-target folding module and GO annotation. Fourth, it supplies the bird eye views of the identification results with info-graphics and grouping information. Fifth, it provides helper functions for database update and auto-recovery to ease system usage and maintenance. Finally, it supports the multi-project and multi-thread management to improve the computational speed.
Proper citation: C-mii (RRID:SCR_010839) Copy
http://www.wageningenur.nl/en/show/Pedimap.htm
A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.
Proper citation: Pedimap (RRID:SCR_010796) Copy
http://evolution.genetics.washington.edu/phylip/software.html
392 phylogeny software packages and 54 free web servers describing all known software for inferring phylogenies (evolutionary trees). Submissions are welcome. Programs are listed by methods available, by computer systems on which they work, cross-referenced by method and by computer system, by ones which analyze particular kinds of data, to show the most recent listings, or to show ones most recently changed.
Proper citation: Phylogeny Programs (RRID:SCR_010797) 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
