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://sourceforge.net/projects/sirnarules/
An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.
Proper citation: siRNArules (RRID:SCR_000096) Copy
http://sourceforge.net/projects/abmining/
Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).
Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy
https://code.google.com/p/snavi/
Desktop application for analysis and visualization of large-scale cell signaling networks.
Proper citation: SNAVI (RRID:SCR_000091) Copy
http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html
Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.
Proper citation: ncdfFlow (RRID:SCR_000009) Copy
http://sourceforge.net/projects/spdesigner/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.
Proper citation: SP-Designer (RRID:SCR_000031) Copy
https://github.com/brendanofallon/SNPSVM/
A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.
Proper citation: SNPSVM (RRID:SCR_000028) Copy
http://sourceforge.net/projects/mysirna/
Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.
Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy
http://microbiology.se/software/megraft/
A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.
Proper citation: Megraft (RRID:SCR_000240) Copy
http://compbio.cs.utoronto.ca/varid/
Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads.
Proper citation: VARiD (RRID:SCR_000241) Copy
http://bioinformatics.psb.ugent.be/webtools/tapir/
Web server designed for prediction of plant microRNA targets.
Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy
http://www.tripos.com/index.php?family=modules,SimplePage,surflex_dock
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software program that screens large libraries of compounds including ligands, and their docking.
Proper citation: Surflex-Dock (RRID:SCR_000196) Copy
https://cran.r-project.org/src/contrib/Archive/MetaDE/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.
Proper citation: MetaDE (RRID:SCR_000199) Copy
http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.
Proper citation: SODOCK (RRID:SCR_000193) Copy
http://exon.gatech.edu/paul/unsplicer/index.htm
An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight.
Proper citation: UnSplicer (RRID:SCR_000226) Copy
https://github.com/matteocereda/RNAmotifs
Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.
Proper citation: RNAmotifs (RRID:SCR_000263) Copy
http://sourceforge.net/projects/protms/
A software tool for the proteomics community that may help improving analysis of proteomic experimental data.
Proper citation: Quant (RRID:SCR_000267) Copy
http://sourceforge.net/projects/biogrinder/
An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.
Proper citation: Grinder (RRID:SCR_000168) Copy
http://www.bioconductor.org/packages/devel/bioc/html/CNTools.html
Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.
Proper citation: CNTools (RRID:SCR_000281) Copy
A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.
Proper citation: GProX (RRID:SCR_000273) Copy
http://peptideprophet.sourceforge.net/
Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.
Proper citation: PeptideProphet (RRID:SCR_000274) 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.
