# An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions

## Documentation for package ‘MultiRNAflow’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CharacterNumbers | Transformation of a vector of integers into a vector of class "character".
ColnamesToFactors | Extraction of factors information and suitable column names creation from the column names of a dataset.
DATAnormalization | Normalization of raw counts (Main Function).
DATAplotBoxplotSamples | Visualization of the distribution of all gene expressions using a boxplot for each sample.
DATAplotExpression1Gene | Plot expression of one gene.
DATAplotExpressionGenes | Plot expression of a subset of genes.
DATAprepSE | Data preparation for exploratory and statistical analysis (Main Function)
DEanalysisGlobal | Realization of the DE analysis (Main Function).
DEanalysisGroup | DE Analysis when samples belong to different biological conditions.
DEanalysisSubData | Sub data of a data.frame
DEanalysisTime | DE analysis when samples belong to different time points only.
DEanalysisTimeAndGroup | DE analysis when samples belong to different biological condition and time points.
DEplotAlluvial | Alluvial graphs of differentially expressed (DE) genes
DEplotBarplot | Barplot of DE genes from a contingency table.
DEplotBarplotFacetGrid | Faceted barplot of specific DE genes
DEplotBarplotTime | Barplot of DE genes per time
DEplotHeatmaps | Heatmaps of DE genes
DEplotVennBarplotGroup | Venn barplot of DE genes across pairs of biological conditions.
DEplotVennBarplotTime | Venn barplot of DE genes across time.
DEplotVolcanoMA | Volcano and MA graphs
DEresultGroup | Intermediate analysis when samples belong to different biological conditions
DEresultGroupPerTime | Intermediate analysis when samples belong to different biological conditions and different time points.
GSEApreprocessing | GSEA preprocessing for official software and online tools.
GSEAQuickAnalysis | GSEA analysis with gprofiler2
HCPCanalysis | Hierarchical clustering analysis with HCPC (Main function)
MFUZZanalysis | Clustering of temporal patterns (Main function).
MFUZZclustersNumber | Automatic choice of the number of clusters to use for the Mfuzz analysis
PCAanalysis | Automatic PCA analysis (Main function)
PCAgraphics | Multiple 2D and 3D PCA graphs.
PCApreprocessing | Reshaped dataset for factorial analysis.
PCArealization | PCA realization
RawCountsSimulation | RNA-seq raw counts data simulation
RawCounts_Antoszewski2022_MOUSEsub500 | Mouse raw counts data
RawCounts_Leong2014_FISSIONsub500wt | Yeast times series raw counts data after stimulation with and without silencing
RawCounts_Schleiss2021_CLLsub500 | Human CCL times series raw counts data after stimulation with and without silencing
RawCounts_Weger2021_MOUSEsub500 | Mouse count data with four biological conditions, six time measurements and 500 genes.
Results_DEanalysis_sub500 | DE results of three dataset
Transcript_HomoSapiens_Database | Homo sapiens transcript database