├── Bioinformatics_Software_Installation.md ├── C_index.R ├── Calculate_time_difference.R ├── Capitalize.R ├── Check_number_of_reads_fastq_gz.sh ├── Conda_Virtual_Environment.txt ├── Create_IDs_for_Cross_Validation.R ├── Download_Data_From_SRA.sh ├── Download_Process_GEO_Datasets.R ├── Figure_to_PPTX_eoffice.R ├── GSVA.R ├── Gene_ID_Conversion ├── Entrez_Gencode_Ensembl_HGNC_IDs.R ├── Homo_Sapiens_Gene_Annotation_ENSEMBL_HGNC_ENTREZ.RDS └── README.md ├── Generate_GMT_File_For_Non_Human_Species.R ├── Get_ENSEMBL_Annotation_biomaRt.R ├── Git ├── Install_R_package_on_Server.R ├── KM_Plot.R ├── Microarray_Normalization.R ├── Mouse_Genome_Annotation_RefSeq_BiomaRt_MGI.R ├── NanoString.R ├── Normal_Violin_Plot.R ├── Notes ├── 10X ├── Single Cell └── server ├── Parse_GENCODE_Annotation.R ├── Portal.R ├── Process_Public_Datasets.R ├── Process_TCGA_Data.R ├── README.md ├── RNAseq_Time_Course_Analysis.R ├── R_Colors.R ├── R_String_Manipulation.R ├── Read_GTF_GFF3.R ├── Reference_Genome.xlsx ├── Rename_files.R ├── SGE_Download_Data_From_ArrayExpress.sh ├── SGE_FastQC_Multiple_Samples.sh ├── SGE_fastp_QC_Multiple_Samples.sh ├── SQLite.R ├── Select_Most_Informative_Probe.R ├── Slurm_MultiQC.sh ├── Slurm_STAR_Alignment.sh ├── Slurm_STAR_Index_Reference.sh ├── Slurm_featureCounts.sh ├── Source_R_Script_From_Github.R ├── TCGA.R ├── TCGA_RNAseq_Clinical.md ├── TPM_FPKM_Conversion.R ├── Target_Evaluation_using_Public_Databases.R ├── Teradata_Studio_SQL.md ├── Transcriptome_Downstream_Analysis_Workflow.R ├── Visualization └── data │ ├── dataForBarPlot.rds │ ├── dataForBarPlot_GO.rds │ ├── dataForBarPlot_KEGG.rds │ ├── dataForBarPlot_Negative.rds │ ├── dataForBarPlot_PDX.rds │ ├── dataForBarPlot_TCGA.rds │ ├── dataForBoxPlot.rds │ ├── dataForBubblePlot.rds │ ├── dataForHeatmap_0and1.rds │ ├── dataForHeatmap_0to1.rds │ ├── dataForHeatmap_eSet.rds │ ├── dataForHeatmap_fcMatrix.rds │ ├── dataForScatterPlot_Feature_Importance.rds │ ├── dataForScatterPlot_Time_Series.rds │ ├── dataForScatterPlot_Treatment_Response.rds │ └── dataForVolcanoPlot.rds ├── detach_R_package.R ├── edgeR.R ├── featureCounts.R ├── ggplot2.R ├── md5sum ├── shiny ├── shinyApp.R └── shiny_functions.R └── xCell_CIBERSORT.R /Bioinformatics_Software_Installation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rli012/BioinfoHub/HEAD/Bioinformatics_Software_Installation.md -------------------------------------------------------------------------------- /C_index.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rli012/BioinfoHub/HEAD/C_index.R -------------------------------------------------------------------------------- /Calculate_time_difference.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rli012/BioinfoHub/HEAD/Calculate_time_difference.R 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