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oneChannelGUI (version 1.38.0)

A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

Description

This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis

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Version

Version

1.38.0

License

Artistic-2.0

Maintainer

Raffaele A Calogero

Last Published

February 15th, 2017

Functions in oneChannelGUI (1.38.0)

Plotting Nts frequency for mapped reads extracted from BAM files

createGeoTarget

Creating a affylmGUI Target starting from a GEO Matrix series file

This function creates files in BED15 format to be loaded on the UCSC browser

graphical interface to edgeR library.

Primary mapping of short reads with Bowtie/Picard for mRNA-seq

Interquantile filtering with a mouse click

graphical interface to limma for alternative splicing detection

graphical interface to RmiR library.

Plotting parents of a GO term with few mouse click

mapping2ensembl

Associating e-level probe sets to entrez gene exonic structure

This function maps on exon-level Probe Selection Region (PSR) starting for the file produced by function oneChannelGUI: Mapping exon level probe sets to Reference Sequences

This function loads Bam files generated by local mapping with bowte in oneChannelGUI

The function executes maSigPro analysis

Raw p-value distribution from limma analysis by a mouse click

Widget to create a target file to load .CEL files

This function coverts the exon intenisty data in a slice index

Removing from exon array gene/exon level probe sets characterized by cross hybridization with other transcripts

Grabbing info about the available expression set

getNGSannotation

Retrieving genome annotation from ENSEMBL

Downloading software for NGS

sample.size.evaluation1

The function executes functions from the sizepower packahe

Plotting Quality scores for mapped reads extracted from BAM files

buildingLocalAnnotation

Updates local gene-level annotation data for gene and exon arrays using the netaffx database

OpenBeadStudioFiles

Read BeadStudio expression data file

Plotting the number of mapped reads extracted from BAM files

Filtering only gene-level probe sets with multiple ensembl transcripts

Graphical interface to APT midas

reformating output of NGS primary tools software

Bovine microRNA data set

The function creates an data frame containing the parameters useful for class prediction

inspecting.one.splice.index

Plotting on the profiles of splice indexes for a transcript cluster ID

Downloading and building chromosome level genomes references for bowtie

Defining t-test regularized p-values

Plotting raw log2 intensities from controls

erankProdAltSpl

Implementation of the Rank Product method for the detection of alternative splicing events

This function allows to combine GEO Matrix Series Files belonging to the same experiment.

Extracting probe ids associated to a specific Gene Ontology term

annotateNGSeset

Associate annotation to NGS data loaded in oneChannelGUI

Creating heat map for maSigPro data with only one treatment condition

A wrapper for makeGCcontent, makeGeneScaffold

This function allows filtering on the basis of variant exons

Mouse microRNA data set

Primary mapping of short reads with Bowtie/Picard for miRNA

Creating a training set and a test set by a mouse click

bayseqInterface

graphical interface to baySeq library.

Extract a column from a tab delimited file with header

rankingConversion

This function transforms intensity data in normalized ranks

stand alone function to generate a scaffold containing only ncRNA location from ENSEMBL

Human microRNA data set

This function plots the sample relations based on multidimensional scaling using the plotMDS.dge edgeR function

This function allows filtering on the basis of the average splice index mean or min difference between two groups

retrieveMirTargets

graphical interface to RmiR.Hs.miRNA library.

Building a list of gene-level GC frequencies

retrievePSRseq1gid

This function, given a gene-level probeset id, retrieves Probe selection Regions, PRS, from RRE db

The function allows the visualization of maSigPro results

Gene/Exon level density plots

This function refines the structure of the genomics peaks, checking for the presence nearby peaks that cna be combined

This function reorganizes single NGS data in a matrix to be used for statistical analysis.

extractmirTargets

Extract miRNA targets showing a opposite regulation with respect to miRNA

This function loads large data set made from tab delimited files

Downloading Bowtie and Picard tools

Rat microRNA data set

Modification of the function immplemented in affylmGUI to generate a topTable

stand alone function to generate a scaffold containing only exon location from ENSEMBL

Graphical interface to metaArray Integrative Correlation function

Filtering by mean of correlation between expression data and miRNA expression changes

makeGeneScaffold

Building a GRange object at chromosome level on UCSC genome data

Filtering a tab delimited file

consistentFilters

This function allows filtering using the combination of multiple paramenters, e.g. MiDAS p-values and Rank Product p-values

Running the affy expresso function with the widget

Subset of genomic regions with ncRNA in Rattus norvegicus

Gene/Exon level density plots

Trimming 3,5 end primers for miRNAs NGS

Subset of genomic regions with ncRNA of Homo sapiens

This function allows to link GeneBank and Entrez Gene ids to gene-level probe set ids

Searching for Gene Ontology enriched terms within a set of differentially expressed genes

Chromosomes lenghts

sample.size.evaluation

The function executes and plots results from ssize and delta fulction from the ssize packahe

standAloneBuildingLocalAnnotation

Creates a data frame with gene-level annotation data for exon arrays using the netaffx database

This function allows to reformat an eSet to be loaded in meV visualization software

Retrieving Reference Sequences from NCBI ftp

This function allows to update the present installation of Bioconductor

This function scale-normalize NGS raw data as described by Robinson and Oshlack Genome Biology 2010, 11:R25

filteringmiRtargets

Subsetting an expression set using a list of gene which are putative targets for a miRNA

linking GEO platforms to available BioC annotations libraries

This function allows to combine two matrices extracted from oneChannelGUI.

This function maps on NCBI Reference sequences spliced exons detected by the function oneChannelGUI: Inspecting splice indexes

This function, given a file containing exon-level probesets retrieves Probe selection Regions, PRS, from RRE db

Reverse interquantile filtering with a mouse click

Box plot of the arrays data available in NormalizeAffyData slot

Filtering an expression set using a set of Entrez genes extracted from Ingenuity Pathways analysis (IPA)

Venn diagrams using two or three lists

Extracting info on the counts associated to a differentially expressed ncRNA gene

Downloading Bowtie prebuilt reference sets

MA and Volcano plots from data present in a limma derived topTable

exonsSpecific2as

Defining the exons associated to the various alternative isoforms

exonTopTableExtract

Extracts data on the basis of a defined t-test regularized p-value

genomeStudioReformat

The present function reformat an expression file exported by Genome Studio in a format that is compatible with oneChannelGUI

inspecting.splice.index

Plotting on a pdf file the profiles of splice indexes

graphical interface apply linear model to two sample groups with batch effect.

Tool to create a merge object for metaArray package

oneChannelGUI-package

Set of functions extending the capability of affylmGUI package

graphical interface to rank product method implemented in RankProd Bioconductor library.

graphical interface to MADS/jetta R library.

The function executes SAM analysis implemented in siggenes bioconductor library

Generating a template A to be uploaded in Ingenuity Pathways analysis (IPA)

This function plots average intensity signals for two group experiment over the genes and transcripts structure mapped on ENSEMBL to identify a specific splicing event

Download the Library files for gene and exon analysis

Subsetting an expression set using a list of Affymetrix ids

intensityFilter

intensity filtering with a mouse click

Starting oneChannelGUI package

This function plots on UCSC genome browser data derived by variantSI filter

This function is used to generate a table containing exon-level probe set data linked to variant exons

A modified version of the function used in affyPLM library

A wrapper to cosie, Corrected Splicing Indices for Exon arrays, that for any given set of new exon array experiments corrects for the observed bias and improves the detection of alternative splicing

erankProdAltSplFilter

Filtering Rank Product results for the detection of alternative splicing events

masigpro.edesign

The function creates an edesign object needed to run maSigPro

Setting to 0 low log2 intensity values generated with plier

Subset of genomic regions with ncRNA of Mus musculus

standAloneAddingAnnotation

Attach to a data frame containing gene-level data derived from Affymetrix exon arrays the annotations derived by netaffx