Files in Kuanhao-Chao/RNASeqR
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
.BBSoptions
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AdditionalClasses_bam.R
R/AdditionalClasses_sam.R
R/AllClasses.R
R/DE_Ballgown_analysis.R
R/DE_DESeq2_analysis.R
R/DE_edgeR_analysis.R
R/Functional_Pathway_GO_KEGG.R
R/LoadMessage.R
R/RNASeqRParam_Bam_show_method.R
R/RNASeqRParam_Sam_show_method.R
R/RNASeqRParam_show_method.R
R/RNASeqR_package.R
R/Update_fastq_gz.R
R/Visualization.R
R/all_steps_interface.R
R/cmd_batch_rnaseq_GO_KEGG.R
R/cmd_batch_rnaseq_differential_analysis.R
R/cmd_batch_rnaseq_environment_set.R
R/cmd_batch_rnaseq_quality_assessment.R
R/cmd_batch_rnaseq_raw_read_process.R
R/rnaseq_raw_read_process_hisat2_samtools_stringtie_ballgown_related.R
R/utility_installtool_rnaseqpipline.R
R/yeast-data.R
README.md
data/yeast.RData
inst/CITATION
man/All_Steps_Interface.Rd
man/All_Steps_Interface_CMD.Rd
man/CheckToolAll.Rd
man/RNASeqDifferentialAnalysis.Rd
man/RNASeqDifferentialAnalysis_CMD.Rd
man/RNASeqEnvironmentSet.Rd
man/RNASeqEnvironmentSet_CMD.Rd
man/RNASeqGoKegg.Rd
man/RNASeqGoKegg_CMD.Rd
man/RNASeqQualityAssessment.Rd
man/RNASeqQualityAssessment_CMD.Rd
man/RNASeqR.Rd
man/RNASeqRParam-class.Rd
man/RNASeqRParam-constructor.Rd
man/RNASeqRParam_Bam-class.Rd
man/RNASeqRParam_Bam-constructor.Rd
man/RNASeqRParam_Sam-class.Rd
man/RNASeqRParam_Sam-constructor.Rd
man/RNASeqReadProcess.Rd
man/RNASeqReadProcess_CMD.Rd
man/Update_Fastq_gz.Rd
man/yeast.Rd
vignettes/RNASeqR.Rmd
vignettes/bibliography.bib
vignettes/figure/Alignment_Report/Alignment_Result_ggplot2.png
vignettes/figure/Alignment_Report/Overall_Mapping_rate_ggplot2.png
vignettes/figure/DE/Heatmap_Plot_pheatmap.png
vignettes/figure/DE/MA_Plot_DESeq2.png
vignettes/figure/DE/PCA/Dimension_PCA_Plot_factoextra.png
vignettes/figure/DE/PCA/PCA_Plot_factoextra.png
vignettes/figure/DE/PCA/PCA_Plot_ggplot2.png
vignettes/figure/DE/Statistical_Results.png
vignettes/figure/DE/Volcano_Plot_graphics.png
vignettes/figure/GO_analysis/GO_CC_Classification_Bar_Plot_clusterProfiler.png
vignettes/figure/GO_analysis/GO_MF_Overrepresentation_Bar_Plot_clusterProfiler.png
vignettes/figure/GO_analysis/GO_MF_Overrepresentation_Dot_Plot_clusterProfiler.png
vignettes/figure/ballgown_MA_Plot_ggplot2.png
vignettes/figure/edgeR_BCV_Plot_edgeR.png
vignettes/figure/edgeR_MDS_Plot_edgeR.png
vignettes/figure/edgeR_MeanVar_Plot_edgeR.png
vignettes/figure/edgeR_Smear_Plot_edgeR.png
vignettes/figure/fastqReport.png
vignettes/figure/input_files_structure.png
vignettes/figure/phenodata_csv.png
vignettes/figure/preDE/Correlation/Correlation_Bar_Plot_PerformanceAnalytics.png
vignettes/figure/preDE/Correlation/Correlation_Dot_Plot_corrplot.png
vignettes/figure/preDE/Correlation/Correlation_Heat_Plot_ggplot2.png
vignettes/figure/preDE/Dispersion_Plot_DESeq2.png
vignettes/figure/preDE/Distribution/Box_Plot_ggplot2.png
vignettes/figure/preDE/Distribution/Violin_Plot_ggplot2.png
vignettes/figure/preDE/Frequency/Frequency_Plot_log_normalized_count_ggplot2.png
vignettes/figure/preDE/Frequency/Frequency_Plot_normalized_count_ggplot2.png
vignettes/figure/preDE/PCA/Dimension_PCA_Plot_factoextra.png
vignettes/figure/preDE/PCA/PCA_Plot_factoextra.png
vignettes/figure/preDE/PCA/PCA_Plot_ggplot2.png
vignettes/figure/transcript_related/Distribution_Transcript_Count_per_Gene_Plot.png
vignettes/figure/transcript_related/Distribution_Transcript_Length_Plot.png
vignettes/figure/whole_file_structure.png
