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://weizhong-lab.ucsd.edu/cd-hit/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CD-HIT (RRID:SCR_007105) Copy
http://bioinf.cs.ucl.ac.uk/software_downloads/biorat/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. An information extraction (IE) tool specifically designed to perform biomedical IE and which is able to locate and analyze both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE.
Proper citation: BioRAT (RRID:SCR_007099) Copy
https://code.google.com/p/swdmr/
A free software using a sliding-window approach to identify differentially methylated regions (DMR) from whole-genome bisulfite sequencing.
Proper citation: swDMR (RRID:SCR_007316) Copy
http://web.bioinformatics.ic.ac.uk/geb/
A Java application developed to visualise distribution of genomic features in high resolution.
Proper citation: GEB (RRID:SCR_007395) Copy
Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.
Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://ngs.ym.edu.tw/ym500/index.php
An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions.
Proper citation: YM500 (RRID:SCR_007429) Copy
http://bmserver.sce.ntu.edu.sg/INVERTER/
Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.
Proper citation: INVERTER (RRID:SCR_007956) Copy
http://genome.ufl.edu/rivalab/pasta/
A complete pipeline for the analysis of alternative splicing using RNA-Sequencing data.
Proper citation: PASTA (RRID:SCR_008770) Copy
http://www.raetschlab.org/suppl/qpalma
An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.
Proper citation: QPALMA (RRID:SCR_008791) Copy
http://r-forge.r-project.org/projects/sequgio/
An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts.
Proper citation: Sequgio (RRID:SCR_008867) Copy
http://lrcv-crp-sante.s3-website-us-east-1.amazonaws.com/
A gene set analysis algorithm for biomarker identification in the cloud.
Proper citation: YunBe (RRID:SCR_008740) Copy
An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.
Proper citation: Textpresso (RRID:SCR_008737) Copy
http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml
A Java-based, Microarray or Genechip data analysis system.
Proper citation: FGDP (RRID:SCR_008910) Copy
http://www.biomedcentral.com/1471-2105/14/357/abstract
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author.
Proper citation: A sample size calculation method (RRID:SCR_009469) Copy
http://www.cibiv.at/~niko/ngc/
A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.
Proper citation: NGC (RRID:SCR_009342) Copy
http://geckoe.sourceforge.net/
A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
Proper citation: Gecko (RRID:SCR_009001) Copy
http://homes.cs.washington.edu/~dcjones/quip/
Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice.
Proper citation: Quip (RRID:SCR_009362) Copy
http://bioinformatics.ua.pt/software/mfcompress/
A compression tool for FASTA and multi-FASTA files.
Proper citation: MFCompress (RRID:SCR_009301) Copy
http://bioinformatics.research.nicta.com.au/software/rlz/
Optimized relative Lempel-Ziv compression of genomes.
Proper citation: RLZ (RRID:SCR_009420) 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.
