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://cbio.ensmp.fr/~ahaury/svn/dream5/html/index.html
Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org).
Proper citation: TIGRESS (RRID:SCR_011977) Copy
Automates the primary analysis of massive parallel sequencing data.
Proper citation: NARWHAL (RRID:SCR_011858) Copy
https://code.google.com/p/orthagogue/
A software tool for high speed estimation of homology relations within and between species in massive data sets.
Proper citation: orthAgogue (RRID:SCR_011979) Copy
http://sourceforge.net/apps/mediawiki/seqgene/?title=SeqGene
An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.
Proper citation: SeqGene (RRID:SCR_011861) Copy
It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.
Proper citation: Oqtans (RRID:SCR_011905) Copy
http://www.reddit.com/r/bioinformatics/
A subreddit dedicated to bioinformatics, computational genomics and systems biology.
Proper citation: reddit (RRID:SCR_011983) Copy
http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas
Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.
Proper citation: Genboree Workbench (RRID:SCR_011864) Copy
https://bioinf.eva.mpg.de/ibis/
An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads.
Proper citation: Ibis (RRID:SCR_011865) Copy
http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://www-huber.embl.de/users/anders/HTSeq/doc/count.html
Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: htseq-count (RRID:SCR_011867) Copy
http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/
Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.
Proper citation: RNAseqViewer (RRID:SCR_011900) Copy
http://pages.cs.wisc.edu/~bsettles/abner/
A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.
Proper citation: ABNER (RRID:SCR_011868) Copy
http://transcriptome.ens.fr/eoulsan/
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
Proper citation: Eoulsan (RRID:SCR_011901) Copy
A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.
Proper citation: FX (RRID:SCR_011902) Copy
http://www.eecs.ucf.edu/~xiaoman/SIOMICS/SIOMICS.html
A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.
Proper citation: SIOMICS (RRID:SCR_011990) Copy
A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.
Proper citation: LitInspector (RRID:SCR_011870) Copy
An open-source program for doing molecular docking.
Proper citation: AutoDock Vina (RRID:SCR_011958) Copy
http://cran.r-project.org/web/packages/vegan/index.html
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Proper citation: vegan (RRID:SCR_011950) Copy
http://www.cs.helsinki.fi/u/lmsalmel/coral/
An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.
Proper citation: Coral (RRID:SCR_011849) Copy
http://scalpel.sourceforge.net/
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).
Proper citation: Scalpel (RRID:SCR_012107) 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.
