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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://i122server.vu-wien.ac.at/CANGS1.1/
A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Proper citation: CANGS (RRID:SCR_011837) Copy
http://topaz.gatech.edu/GeneTack/cgi/print_page.cgi?fn=db_home.html&title=Frameshift%20Database
Tools for frameshift prediction and a frameshift database.
Proper citation: GeneTack (RRID:SCR_011953) Copy
Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species.
Proper citation: JiffyNet (RRID:SCR_011954) Copy
Online community for industry news and careers for life science professionals.
Proper citation: BioSpace (RRID:SCR_012010) Copy
https://github.com/najoshi/sabre
Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.
Proper citation: sabre (RRID:SCR_011843) Copy
http://tfclass.bioinf.med.uni-goettingen.de/tfclass
Database that classifies human transcription factors based on the characteristics of their DNA-binding domains. It comprises six levels (superclasses, classes, families, subfamilies, genera and factor species), two of which are optional (subfamilies and factor species). The full classification can also be obtained as html document and as ontology in obo-format., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TFClass (RRID:SCR_012018) Copy
http://tagcleaner.sourceforge.net/
A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.
Proper citation: TagCleaner (RRID:SCR_011846) Copy
International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy.
Proper citation: INSDC (RRID:SCR_011967) Copy
http://rnaseq-mats.sourceforge.net/
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy
http://bioconductor.org/help/mailing-list/
This mailing list is for announcements about Bioconductor and the availability of new code and questions and answers about problems and solutions using Bioconductor.
Proper citation: Bioconductor mailing list (RRID:SCR_012915) Copy
https://www.ncbi.nlm.nih.gov/assembly
Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ).
Proper citation: NCBI Assembly Archive Viewer (RRID:SCR_012917) Copy
A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.
Proper citation: GRASSIUS (RRID:SCR_012999) Copy
http://bioinfo2.ugr.es/NGSmethDB/
A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.
Proper citation: NGSmethDB (RRID:SCR_012847) Copy
A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute.
Proper citation: GenomeView (RRID:SCR_012968) Copy
Ratings or validation data are available for this resource
http://ccb.jhu.edu/software/tophat/index.shtml
Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
Proper citation: TopHat (RRID:SCR_013035) Copy
http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi
Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.
Proper citation: MitoBreak (RRID:SCR_012949) Copy
http://www.bioconductor.org/packages/release/bioc/html/minfi.html
Software tools for analyzing and visualizing Illumina''s 450k array data.
Proper citation: minfi (RRID:SCR_012830) Copy
http://www.bioconductor.org/packages/release/bioc/html/affy.html
Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.
Proper citation: affy (RRID:SCR_012835) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
Proper citation: KEGG (RRID:SCR_012773) Copy
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