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on page 1 showing 20 out of 43 results

    affydata

Cite this (affydata, RRID:SCR_016976)

URL: http://bioconductor.org/packages/release/data/experiment/html/affydata.html

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

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

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    affy

Cite this (affy, RRID:SCR_012835)

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

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

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.

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Cite this (Bioconductor, RRID:SCR_006442)

URL: http://www.bioconductor.org/

Resource Type: Resource, data analysis software, data processing software, software library, database, software application, software repository, catalog, software resource, software toolkit, data or information resource

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

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Cite this (Biostrings, RRID:SCR_016949)

URL: https://bioconductor.org/packages/release/bioc/html/Biostrings.html

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

Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

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    braincog

Cite this (braincog, RRID:SCR_015871)

URL: https://github.com/ChristofSeiler/braincog

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

Software package to elucidate complex interactions between subsets of neuroanatomical features and subsets of cognitive features. briancog specializes in differential correlation analysis.

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Cite this (clusterProfiler, RRID:SCR_016884)

URL: http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

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

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

  • From Current Category

    clustree

Cite this (clustree, RRID:SCR_016293)

URL: https://CRAN.R-project.org/package=clustree

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

Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties.

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    ClustVis

Cite this (ClustVis, RRID:SCR_017133)

URL: https://biit.cs.ut.ee/clustvis/

Resource Type: Resource, data analysis service, data access protocol, production service resource, web service, analysis service resource, service resource, software resource

Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.

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    devtools

Cite this (devtools, RRID:SCR_016961)

URL: https://cran.r-project.org/web/packages/devtools/index.html

Resource Type: Resource, software resource, software toolkit

Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.

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    dndSCV

Cite this (dndSCV, RRID:SCR_017093)

URL: https://github.com/im3sanger/dndscv

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

Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.

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    dplyr

Cite this (dplyr, RRID:SCR_016708)

URL: https://cran.r-project.org/web/packages/dplyr/index.html

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

Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.

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    FlowSOM

Cite this (FlowSOM, RRID:SCR_016899)

URL: https://github.com/SofieVG/FlowSOM

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

Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.

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    GAGE

Cite this (GAGE, RRID:SCR_017067)

URL: http://bioconductor.org/packages/gage/

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

Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.

  • From Current Category

Cite this (GenomicFeatures, RRID:SCR_016960)

URL: http://bioconductor.org/packages/GenomicFeatures/

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

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

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Cite this (Genomic Ranges, RRID:SCR_017051)

URL: http://bioconductor.org/packages/GenomicRanges/

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

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

  • From Current Category

    geomorph

Cite this (geomorph, RRID:SCR_016482)

URL: https://cran.r-project.org/web/packages/geomorph/index.html

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

Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.

  • From Current Category

    ggplot2

Cite this (ggplot2, RRID:SCR_014601)

URL: https://cran.r-project.org/web/packages/ggplot2/index.html

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

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

  • From Current Category

    glmmADMB

Cite this (glmmADMB, RRID:SCR_016859)

URL: http://glmmadmb.r-forge.r-project.org/

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

Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions.

  • From Current Category

    Goseq

Cite this (Goseq, RRID:SCR_017052)

URL: https://bioconductor.org/packages/release/bioc/html/goseq.html

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

Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.

  • From Current Category

Cite this (Heatmapper, RRID:SCR_016974)

URL: http://www2.heatmapper.ca/

Resource Type: Resource, web service, software resource, data processing software, data access protocol, software application

Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.

  • From Current Category

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