Man pages for anilchalisey/parseR
Pipeline for Analysis of RNA-seq in R
| aggregate_fqc | Aggregate and summarise FastQC reports for multiple samples |
| align_rna | Alignment of RNA-seq reads |
| annotation | SAF file for human hg19 genome |
| count_reads | Count reads in bam files using featureCounts |
| create_contrast | Design and contrast matrices |
| create_fqreport | Create a QC report |
| create_hmp | Heatmap of most differential genes. |
| create_maplot | Create MA plot |
| create_mds | Create multi-dimensional scaling plot from DGE object |
| create_pca | Create principal component analysis plot from DDS object |
| create_se | Create Summarized Experiment |
| deseq2_norm | Count normalisation using DESeq2 |
| deseq2_pipe | Pipeline for DESeq2 analysis |
| edger_norm | Count normalisation using edgeR |
| edger_pipe | Pipeline for edgeR analysis |
| homer_known | Parse HOMER motif files |
| limma_pipe | Pipeline for limma+voom analysis |
| load_samples | Load sample metadata file |
| make_bigwig | Create bigwig files from BAM |
| make_venn | Make venn diagrams showing overlapping gene lists |
| plot_fqc | Plot FastQC Results |
| process_counts | Pre-processing of counts |
| read_fastqc | Read a single FastQC data file |
| read_multifastqc | Read a a directory of FastQC data files |
| run_deseq2 | Run DESeq2 analysis |
| run_diff | Run the differential analysis pipeline |
| run_edger | Run edgeR-QLF |
| run_fastqc | Run FastQC |
| run_goseq | Gene ontology and pathway analysis of DE genes |
| run_hisat2 | Wrapper script to run HISAT2. |
| run_homer | Run HOMER for promoter motif enrichment |
| run_limma | Run limma+voom |
| run_sambambadup | Mark duplicates in BAM file |
| run_samsort | Wrapper scripts for SAMtools functions |
