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://genome.sph.umich.edu/wiki/Generic_Exome_Analysis_Plan
Outline of a generic plan for analysis of a whole exome sequencing project.
Proper citation: Generic Exome Analysis Plan (RRID:SCR_009656) Copy
http://www.stanford.edu/group/wonglab/SpliceMap/
A de novo splice junction discovery and alignment tool.
Proper citation: SpliceMap (RRID:SCR_009650) Copy
http://bioen-compbio.bioen.illinois.edu/TrueSight/
Self-training Algorithm for Splice Junction Detection using RNA-seq.
Proper citation: TrueSight (RRID:SCR_009835) Copy
http://www.allseq.com/default.aspx
Free online tools to find the best Sequencing Service provider for your project.
Proper citation: AllSeq (RRID:SCR_010053) Copy
http://dna.engr.uconn.edu/?page_id=105
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
Proper citation: IsoEM (RRID:SCR_009993) Copy
http://code.google.com/p/bitseq/
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
Proper citation: BitSeq (RRID:SCR_009904) Copy
A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
Proper citation: BEAST (RRID:SCR_010228) Copy
http://hkbic.cuhk.edu.hk/software/abmapper
A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.
Proper citation: ABMapper (RRID:SCR_010242) Copy
http://htsvipr.sourceforge.net/
A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
Proper citation: vipR (RRID:SCR_010685) Copy
http://www.genome.umd.edu/masurca.html
A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MaSuRCA (RRID:SCR_010691) Copy
http://bioinformatics.research.nicta.com.au/software/gossamer/
A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability.
Proper citation: Gossamer (RRID:SCR_010612) Copy
http://www.bcgsc.ca/platform/bioinfo/software/abyss
Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.
Proper citation: ABySS (RRID:SCR_010709) Copy
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0023501
An algorithm for de novo genome assembly with short paired-end reads.
Proper citation: Meraculous (RRID:SCR_010700) Copy
http://www.bio.ifi.lmu.de/contextmap
A context-based approach to identify the most likely mapping for RNA-seq experiments.
Proper citation: ContextMap (RRID:SCR_010496) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CRAC (RRID:SCR_010652) Copy
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
Proper citation: Geneious (RRID:SCR_010519) Copy
http://www.cbrc.kaust.edu.sa/hmcan/
A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data.
Proper citation: HMCan (RRID:SCR_010858) Copy
http://mirtar.mbc.nctu.edu.tw/human/
An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.
Proper citation: miRTar (RRID:SCR_010851) Copy
http://www.cos.uni-heidelberg.de/index.php/n.ha
Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.
Proper citation: COPS (RRID:SCR_010852) Copy
http://woldlab.caltech.edu/wiki/RNASeq#Dual-use_E-RANGE
A Python package for doing RNA-seq and ChIP-seq (hence the dual-use).
Proper citation: E-RANGE (RRID:SCR_010856) 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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
