Files in RNASeqR

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

.BBSoptions

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

data/yeast.RData

R/cmd_batch_rnaseq_raw_read_process.R R/utility_installtool_rnaseqpipline.R R/DE_DESeq2_analysis.R R/cmd_batch_rnaseq_GO_KEGG.R R/Update_fastq_gz.R R/RNASeqRParam_Sam_show_method.R R/RNASeqRParam_show_method.R R/RNASeqR_package.R R/AdditionalClasses_sam.R R/cmd_batch_rnaseq_quality_assessment.R R/Visualization.R R/DE_Ballgown_analysis.R R/LoadMessage.R R/DE_edgeR_analysis.R R/RNASeqRParam_Bam_show_method.R R/Functional_Pathway_GO_KEGG.R R/AllClasses.R R/cmd_batch_rnaseq_environment_set.R R/yeast-data.R R/AdditionalClasses_bam.R R/rnaseq_raw_read_process_hisat2_samtools_stringtie_ballgown_related.R R/all_steps_interface.R R/cmd_batch_rnaseq_differential_analysis.R

vignettes/bibliography.bib

vignettes/RNASeqR.Rmd

vignettes/figure/edgeR_MDS_Plot_edgeR.png

vignettes/figure/fastqReport.png

vignettes/figure/edgeR_MeanVar_Plot_edgeR.png

vignettes/figure/edgeR_Smear_Plot_edgeR.png

vignettes/figure/input_files_structure.png

vignettes/figure/edgeR_BCV_Plot_edgeR.png

vignettes/figure/whole_file_structure.png

vignettes/figure/ballgown_MA_Plot_ggplot2.png

vignettes/figure/phenodata_csv.png

vignettes/figure/transcript_related/Distribution_Transcript_Count_per_Gene_Plot.png

vignettes/figure/transcript_related/Distribution_Transcript_Length_Plot.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/GO_analysis/GO_CC_Classification_Bar_Plot_clusterProfiler.png

vignettes/figure/DE/MA_Plot_DESeq2.png

vignettes/figure/DE/Volcano_Plot_graphics.png

vignettes/figure/DE/Heatmap_Plot_pheatmap.png

vignettes/figure/DE/Statistical_Results.png

vignettes/figure/DE/PCA/PCA_Plot_factoextra.png

vignettes/figure/DE/PCA/PCA_Plot_ggplot2.png

vignettes/figure/DE/PCA/Dimension_PCA_Plot_factoextra.png

vignettes/figure/Alignment_Report/Overall_Mapping_rate_ggplot2.png

vignettes/figure/Alignment_Report/Alignment_Result_ggplot2.png

vignettes/figure/preDE/Dispersion_Plot_DESeq2.png

vignettes/figure/preDE/Frequency/Frequency_Plot_normalized_count_ggplot2.png

vignettes/figure/preDE/Frequency/Frequency_Plot_log_normalized_count_ggplot2.png

vignettes/figure/preDE/PCA/PCA_Plot_factoextra.png

vignettes/figure/preDE/PCA/PCA_Plot_ggplot2.png

vignettes/figure/preDE/PCA/Dimension_PCA_Plot_factoextra.png

vignettes/figure/preDE/Distribution/Box_Plot_ggplot2.png

vignettes/figure/preDE/Distribution/Violin_Plot_ggplot2.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

man/RNASeqQualityAssessment_CMD.Rd man/RNASeqRParam_Sam-class.Rd man/RNASeqGoKegg_CMD.Rd man/RNASeqReadProcess_CMD.Rd man/CheckToolAll.Rd man/RNASeqGoKegg.Rd man/RNASeqEnvironmentSet_CMD.Rd man/RNASeqRParam-class.Rd man/RNASeqDifferentialAnalysis.Rd man/RNASeqRParam_Bam-constructor.Rd man/RNASeqRParam-constructor.Rd man/All_Steps_Interface_CMD.Rd man/RNASeqReadProcess.Rd man/RNASeqR.Rd man/RNASeqEnvironmentSet.Rd man/All_Steps_Interface.Rd man/RNASeqRParam_Sam-constructor.Rd man/yeast.Rd man/Update_Fastq_gz.Rd man/RNASeqDifferentialAnalysis_CMD.Rd man/RNASeqRParam_Bam-class.Rd man/RNASeqQualityAssessment.Rd

inst/CITATION

inst/doc/RNASeqR.R

inst/doc/RNASeqR.html

inst/doc/RNASeqR.Rmd

RNASeqR documentation built on Nov. 8, 2020, 7:49 p.m.