Man pages for anilchalisey/rseqR
RNA-seq data processing pipeline
| annotate_data | Annotate gene data |
| build_index | Build index for mapping using Salmon |
| check_sample | Check that targets file contains the necessary info in the... |
| deseq2_analysis | Run DESeq2 analysis on RNA-seq count data |
| edger_analysis | Run edgeR analysis on RNA-seq count data |
| exploratory_analysis_deseq2 | Exploratory analysis of DESeq2 data |
| exploratory_analysis_edger | Exploratory analysis of edgeR data |
| limma_voom_analysis | Run Limma-voom analysis on RNA-seq count data |
| make_heatmap | Create heatmap with clustering of samples and genes for DEGs |
| make_MA | Create MA plot |
| make_PCA | Create PCA plot for transformed data |
| make_scree | Create scree plot from prcomp data |
| make_upset | Plot intersections of list of DE genes |
| make_volcano | Create Volcano Plot |
| pathway_analysis | Title |
| pipe | Pipe operator |
| read_salmon | Read the run info from Salmon output |
| run_dea | Run differential expression analysis |
| run_fastqc | QC reports for fastq files using FastQC |
| run_multiqc | Generate MultiQC report for FastQC |
| run_salmon | Quantify transcript abundances using Salmon |
| run_tximport | Wrapper function to run tximport |
| sanity_check | Import the metadata and check it is correct |
| trim_fastq | An R-based wrapper for Trim Galore! |
