Reference

Pipeline functions

run_chip()

Run ChIP-seq analysis

run_atac()

Run ATAC-seq analysis

align_dna()

Alignment of DNA-seq reads

Data import functions

check_sample()

Check that targets file contains the necessary info in the right format

sanity_check()

Import the metadata and check it is correct

FASTQ analysis

run_fastqc()

QC reports for fastq files using FastQC

trim_fastq()

An R-based wrapper for fastp

run_multiqc()

Generate MultiQC report for FastQC

HISAT2 functions

build_index()

Build insex for HISAT2

run_hisat2()

Wrapper script to run HISAT2.

BAM file manipulation functions

run_sambambadup()

Mark duplicates in BAM file

run_samsort() run_samindex() run_samview() run_samflagstat()

Wrapper scripts for SAMtools functions

shift_bam()

Shift ATAC-seq reads

run_featurecounts()

Count reads in bam files using featureCounts

create_bw()

Create bigwig files

Alignment QC functions

cc_chip()

Create cross-correlation plots for ChIP-seq data

fl_atac()

Create fragment size plots for ATAC-seq data

qc_alignment()

Generate some alignment statistics on reads

qc_alignment2()

Perform alignment statistics on reads

annotate_peaks()

Annotation of peaks

consensus_peaks()

Consensus peaks

run_macs2()

Perform peakcalling with MACS2

plot_peaksummary()

Plots of peak width and distance to TSS

Differential analysis

deseq2_analysis()

Run DESeq2 analysis on ChIP/ATAC-seq count data

exploratory_analysis()

Exploratory analysis of DESeq2 data

Plotting functions

make_MA()

Create MA plot

make_PCA()

Create PCA plot for transformed data

make_scree()

Create scree plot from prcomp data

Miscellaneous functions

run_great()

GREAT analysis

peak2Granges() Granges2df() Granges2saf()

File conversions

chain

LiftOver chain file in rda format for conversion from hg38 to hg19