Man pages for anilchalisey/chompR
ChIP and ATAC-seq data processing pipeline
| align_dna | Alignment of DNA-seq reads |
| annotate_peaks | Annotation of peaks |
| build_index | Build insex for HISAT2 |
| cc_chip | Create cross-correlation plots for ChIP-seq data |
| chain | LiftOver chain file in rda format for conversion from hg38 to... |
| check_sample | Check that targets file contains the necessary info in the... |
| consensus_peaks | Consensus peaks |
| create_bw | Create bigwig files |
| deseq2_analysis | Run DESeq2 analysis on ChIP/ATAC-seq count data |
| exploratory_analysis | Exploratory analysis of DESeq2 data |
| fl_atac | Create fragment size plots for ATAC-seq data |
| make_MA | Create MA plot |
| make_PCA | Create PCA plot for transformed data |
| make_scree | Create scree plot from prcomp data |
| peak2Granges | File conversions |
| pipe | Pipe operator |
| plot_peaksummary | Plots of peak width and distance to TSS |
| qc_alignment | Generate some alignment statistics on reads |
| qc_alignment2 | Perform alignment statistics on reads |
| run_atac | Run ATAC-seq analysis |
| run_chip | Run ChIP-seq analysis |
| run_fastqc | QC reports for fastq files using FastQC |
| run_featurecounts | Count reads in bam files using featureCounts |
| run_great | GREAT analysis |
| run_hisat2 | Wrapper script to run HISAT2. |
| run_macs2 | Perform peakcalling with MACS2 |
| run_multiqc | Generate MultiQC report for FastQC |
| run_sambambadup | Mark duplicates in BAM file |
| run_samsort | Wrapper scripts for SAMtools functions |
| sanity_check | Import the metadata and check it is correct |
| shift_bam | Shift ATAC-seq reads |
| trim_fastq | An R-based wrapper for fastp |
