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 |
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