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on page 1 showing 20 out of 283 results

    (at)Note

Cite this ((at)Note, RRID:SCR_005342)

URL: http://darwin.di.uminho.pt/anote2/wiki/index.php/Main_Page

Resource Type: Resource, software resource, software application, text-mining software

THIS RESOURCE IS NO LONGER AVAILABLE. Documented September 18, 2017. Text Mining platform that copes with major Information Retrieval and Information Extraction tasks and promotes multi-disciplinary research. It aims to provide support to three different usage roles: biologists, text miners and application developers. The workbench supports the retrieval, processing and annotation of documents as well as their analysis at different levels.

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    4Peaks

Cite this (4Peaks, RRID:SCR_000015)

URL: http://nucleobytes.com/index.php/4peaks

Resource Type: Resource, software resource, software application

Software application for viewing and editing sequence trace files.

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Cite this (AbundantOTU+, RRID:SCR_016527)

URL: http://omics.informatics.indiana.edu/AbundantOTU/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

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Cite this (AdapterRemoval, RRID:SCR_011834)

URL: https://github.com/MikkelSchubert/adapterremoval

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software program to remove residual adapter sequences from next generation sequencing reads.

  • From Current Category

Cite this (AdaptiveCrawler, RRID:SCR_000573)

URL: http://bsec.ornl.gov/AdaptiveCrawler.shtml

Resource Type: Resource, software resource, data acquisition software, data processing software, software application

A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.

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Cite this (Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS, RRID:SCR_016657)

URL: https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Resource Type: Resource, data analysis software, data processing software, software application, data analytics software, software toolkit, software resource, data acquisition software

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

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Cite this (AltAnalyze - Alternative Splicing Analysis Tool, RRID:SCR_002951)

URL: http://www.altanalyze.org/

Resource Type: Resource, software resource, software application

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

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    ANDES

Cite this (ANDES, RRID:SCR_002791)

URL: http://andestools.sourceforge.net/

Resource Type: Resource, software resource, software application, data analysis software, data processing software, software toolkit

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

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    Annotare

Cite this (Annotare, RRID:SCR_000319)

URL: http://code.google.com/p/annotare/

Resource Type: Resource, software resource, software application, standalone software

A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

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    Apollo

Cite this (Apollo, RRID:SCR_001936)

URL: http://gmod.org/wiki/Apollo

Resource Type: Resource, software resource, software application

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.

  • From Current Category

    ARACNE

Cite this (ARACNE, RRID:SCR_002180)

URL: http://wiki.c2b2.columbia.edu/califanolab/index.php/Software/ARACNE

Resource Type: Resource, software resource, software application

An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

  • From Current Category

    asSeq

Cite this (asSeq, RRID:SCR_001625)

URL: http://bios.unc.edu/~weisun/software/asSeq.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software, source code

Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq

  • From Current Category

Cite this (AutoAssemblyD, RRID:SCR_001087)

URL: http://sourceforge.net/projects/autoassemblyd/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

  • From Current Category

    Babel

Cite this (Babel, RRID:SCR_004307)

URL: http://taylorlab.ucsf.edu/software_data.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts

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    BAC

Cite this (BAC, RRID:SCR_001067)

URL: http://www.bioconductor.org/packages/release/bioc/html/BAC.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

  • From Current Category

    BAIT

Cite this (BAIT, RRID:SCR_000511)

URL: http://sourceforge.net/projects/bait/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

  • From Current Category

    bamova

Cite this (bamova, RRID:SCR_000510)

URL: http://www.uwyo.edu/buerkle/software/bamova/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

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    BAMseek

Cite this (BAMseek, RRID:SCR_000672)

URL: https://code.google.com/p/bamseek/

Resource Type: Resource, data visualization software, software application, data processing software, software resource

A Large File Viewer for BAM and SAM alignment files.

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    BHC

Cite this (BHC, RRID:SCR_006399)

URL: http://master.bioconductor.org/packages/2.13/bioc/html/BHC.html

Resource Type: Resource, software resource, software application, data processing software

Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets.

  • From Current Category

Cite this (BIDs Validator, RRID:SCR_017255)

URL: https://github.com/bids-standard/bids-validator

Resource Type: Resource, software resource, software application, data processing software

Software validation tool that checks submitted folder structure for compliance to BIDs data standard. Validates Brain Imaging Data Structure.

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