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/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
http://www.stat.purdue.edu/~doerge/software/TSPM.R
Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.
Proper citation: TSPM.R (RRID:SCR_012021) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
http://www.nature.com/nmeth/journal/v5/n3/extref/nmeth.1184-S2.pdf
Software for decoding error-correcting barcodes.
Proper citation: Standalone hamming (RRID:SCR_012025) Copy
http://sourceforge.net/projects/seqexpress/
A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.
Proper citation: SeqExpress (RRID:SCR_004013) Copy
http://genomics.princeton.edu/AndolfattoLab/MSG.html
A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.
Proper citation: MSG (RRID:SCR_004161) 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://sourceforge.net/projects/hlaseq/
An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.
Proper citation: HLASeq (RRID:SCR_004185) Copy
http://pass.cribi.unipd.it/cgi-bin/pass.pl
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
Proper citation: PASS-bis (RRID:SCR_004176) Copy
http://www.cs.gsu.edu/~serghei/?q=drut
Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.
Proper citation: DRUT (RRID:SCR_004351) Copy
http://www.sanger.ac.uk/resources/software/act/
A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.
Proper citation: ACT: Artemis Comparison Tool (RRID:SCR_004507) Copy
http://compbio.cs.wayne.edu/software/squeezambler/
Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.
Proper citation: Squeezambler (RRID:SCR_004385) Copy
Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
Proper citation: SNiPer-HD (RRID:SCR_004383) 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.
