DEGreport-package |
Deprecated functions in package DEGreport |
as.DEGSet |
DEGSet |
as.DEGSet-method |
DEGSet |
createReport |
Create report of RNAseq DEG anlaysis |
deg |
Method to get all table stored for an specific comparison |
deg-method |
Method to get all table stored for an specific comparison |
degCheckFactors |
Distribution of gene ratios used to calculate Size Factors. |
degColors |
Make nice colors for metadata |
degComps |
Automatize the use of 'results()' for multiple comparisons |
degCorCov |
Calculate the correlation relationshipt among all covariates in the metadata table |
degCorrect |
Method to get the default table to use. |
degCorrect-method |
Method to get the default table to use. |
degCovariates |
Find correlation between pcs and covariates |
degDefault |
Method to get the default table to use. |
degDefault-method |
Method to get the default table to use. |
degFilter |
Filter genes by group |
degMA |
MA-plot from base means and log fold changes |
degMB |
Distribution of expression of DE genes compared to the background |
degMDS |
Plot MDS from normalized count data |
degMean |
Distribution of pvalues by expression range |
degMerge |
Integrate data comming from degPattern into one data object |
degMV |
Correlation of the standard desviation and the mean of the abundance of a set of genes. |
degObj |
Create a deg object that can be used to plot expression values at shiny server:runGist(9930881) |
degPatterns |
Make groups of genes using expression profile. |
degPCA |
smart PCA from count matrix data |
degPlot |
Plot top genes allowing more variables to color and shape points |
degPlotCluster |
Plot clusters from degPattern function output |
degPlotWide |
Plot selected genes on a wide format |
degQC |
Plot main figures showing p-values distribution and mean-variance correlation |
DEGreport |
Deprecated functions in package DEGreport |
degResults |
Complete report from DESeq2 analysis |
DEGSet |
DEGSet |
DEGSet-class |
DEGSet |
degSignature |
Plot gene signature for each group and signature |
degSummary |
Print Summary Statistics of Alpha Level Cutoffs |
degVar |
Distribution of pvalues by standard desviation range |
degVB |
Distribution of the standard desviation of DE genes compared to the background |
degVolcano |
Create volcano plot from log2FC and adjusted pvalues data frame |
geneInfo |
data.frame with chromose information for each gene |
geom_cor |
Add correlation and p-value to a ggplot2 plot |
humanGender |
DGEList object for DE genes betwen Male and Females |
significants |
Method to get the significant genes |
significants-method |
Method to get the significant genes |