Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.

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• SciCrunch
• 17 years ago - by Anonymous

Database of bacteriophage gene regulation elements, genes, and genomes. Data are collected from scientific papers and cross-referenced with other database resources. The database can be searched using keywords or browsed by phage genome. Sets of regulatory sequences can browsed and exported in various formats.

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• RRID-Legacy
• 10 years ago - submitted by Ivan Erill

Software R package provides some basic functions for filtering genes.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.

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• SciCrunch
• 17 years ago - by Anonymous

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome

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• SciCrunch
• 17 years ago - by Anonymous

Software library of core preprocessing routines.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

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• SciCrunch
• 12 years ago - by Anonymous

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

• RRID-Legacy
• 10 years ago - submitted by Mihai Capotă

Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).

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• SciCrunch
• 13 years ago - by Anonymous

Medical research facility that supports research programs by providing access to sophisticated microscopes for digital imaging, as well as training, assistance and guidance. The core facility offers expertise, training and assistance in advanced biological microscopic imaging techniques and use of complex image processing software, use of well-maintained, aligned, and calibrated microscopic equipment, and troubleshooting of equipment and experimental problems.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Matlab toolbox for analyzing neuronal electrophysiology data and constructing databases.

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• SciCrunch
• 13 years ago - by Anonymous

Core facility that provides diverse screening instrumentation, compound libraries and expertise on high throughput screens and automation in support of collaborative, and user- or facility-driven screening projects. The facility collaborates with a number of partners to develop molecular therapies. Services available include consultation for high throughput screening approaches, conversion of assays to automation compatible formats and data analysis.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package provides environment for Time-Frequency analysis of 1-D signals.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software that provides utilities for flow cytometry data.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. The server uses publicly available genotype data for over 15,000 markers. It facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps. The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.

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• SciCrunch
• 17 years ago - by Anonymous

Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.

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• SciCrunch
• 13 years ago - by Anonymous

GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible

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• SciCrunch
• 15 years ago - by Anonymous