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oneChannelGUI (version 1.36.0)

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

1.36.0

License

Artistic-2.0

Maintainer

Raffaele A Calogero

Last Published

February 15th, 2017

Functions in oneChannelGUI (1.36.0)

Filtering only gene-level probe sets with multiple ensembl transcripts

Downloading Bowtie prebuilt reference sets

Bovine microRNA data set

buildingLocalAnnotation

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

Graphical interface to APT midas

Trimming 3,5 end primers for miRNAs NGS

Downloading and building chromosome level genomes references for bowtie

bayseqInterface

graphical interface to baySeq library.

Downloading Bowtie and Picard tools

annotateNGSeset

Associate annotation to NGS data loaded in oneChannelGUI

createGeoTarget

Creating a affylmGUI Target starting from a GEO Matrix series file

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

Creating heat map for maSigPro data with only one treatment condition

Chromosomes lenghts

This function allows to combine two matrices extracted from oneChannelGUI.

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

Extract a column from a tab delimited file with header

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

consistentFilters

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

graphical interface to edgeR library.

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

erankProdAltSpl

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

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

Plotting Nts frequency for mapped reads extracted from BAM files

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

Plotting Quality scores for mapped reads extracted from BAM files

Plotting the number of mapped reads extracted from BAM files

inspecting.one.splice.index

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

Human microRNA data set

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

Interquantile filtering with a mouse click

Graphical interface to metaArray Integrative Correlation function

The function allows the visualization of maSigPro results

Gene/Exon level density plots

extractmirTargets

Extract miRNA targets showing a opposite regulation with respect to miRNA

Extracting probe ids associated to a specific Gene Ontology term

Gene/Exon level density plots

getNGSannotation

Retrieving genome annotation from ENSEMBL

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

Subset of genomic regions with ncRNA in Rattus norvegicus

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

filteringmiRtargets

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

Filtering a tab delimited file

Download the Library files for gene and exon analysis

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

Subsetting an expression set using a list of Affymetrix ids

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

Setting to 0 low log2 intensity values generated with plier

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

Plotting parents of a GO term with few mouse click

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

Rat microRNA data set

graphical interface to MADS/jetta R library.

erankProdAltSplFilter

Filtering Rank Product results for the detection of alternative splicing events

genomeStudioReformat

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

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

linking GEO platforms to available BioC annotations libraries

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

exonsSpecific2as

Defining the exons associated to the various alternative isoforms

graphical interface to limma for alternative splicing detection

exonTopTableExtract

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

Building a list of gene-level GC frequencies

makeGeneScaffold

Building a GRange object at chromosome level on UCSC genome data

masigpro.edesign

The function creates an edesign object needed to run maSigPro

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

reformating output of NGS primary tools software

The function executes maSigPro analysis

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

Subset of genomic regions with ncRNA of Homo sapiens

This function loads large data set made from tab delimited files

Subset of genomic regions with ncRNA of Mus musculus

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

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

rankingConversion

This function transforms intensity data in normalized ranks

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

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

sample.size.evaluation

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

sample.size.evaluation1

The function executes functions from the sizepower packahe

retrievePSRseq1gid

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

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

graphical interface to RmiR library.

Reverse interquantile filtering with a mouse click

standAloneBuildingLocalAnnotation

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

Widget to create a target file to load .CEL files

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

Box plot of the arrays data available in NormalizeAffyData slot

Retrieving Reference Sequences from NCBI ftp

retrieveMirTargets

graphical interface to RmiR.Hs.miRNA library.

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

Defining t-test regularized p-values

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

inspecting.splice.index

Plotting on a pdf file the profiles of splice indexes

intensityFilter

intensity filtering with a mouse click

mapping2ensembl

Associating e-level probe sets to entrez gene exonic structure

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

Mouse microRNA data set

A modified version of the function used in affyPLM library

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

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

Plotting raw log2 intensities from controls

Grabbing info about the available expression set

Modification of the function immplemented in affylmGUI to generate a topTable

This function allows to update the present installation of Bioconductor

Venn diagrams using two or three lists

A wrapper for makeGCcontent, makeGeneScaffold

Downloading software for NGS

Primary mapping of short reads with Bowtie/Picard for miRNA

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

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

Running the affy expresso function with the widget

oneChannelGUI-package

Set of functions extending the capability of affylmGUI package

Starting oneChannelGUI package

The function executes SAM analysis implemented in siggenes bioconductor library

standAloneAddingAnnotation

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

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

This function allows filtering on the basis of variant exons

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

This function coverts the exon intenisty data in a slice index