• peak_files: A list of path to peak files or GRanges objects with
  the peaks to analyse. Currently, only peak files from MACS2/3
  (.narrowPeak) and SEACR (.bed) are supported. ENCODE file IDs
  can also be provided to automatically fetch peak file(s) from the
  ENCODE database.
• reference_index: An integer specifying the index of the reference
  dataset in the peak_files list to use as reference for various
  comparisons. (default = 1)
• genome_build: A character string or a BSgenome object specifying
  the genome build of the datasets. At the moment, only hg38 and hg19
  are supported as abbreviated input.
• out_dir: A character string specifying the output directory to save
  the HTML report and other files.

• alignment_files: A list of path to alignment files or
  Rsamtools::BamFile objects with the alignment sequences to analyse.
  Alignment files are used to calculate read-related metrics like FRiP
  score. ENCODE file IDs can also be provided to automatically fetch
  alignment file(s) from the ENCODE database.
• exp_labels: A character vector of labels for each peak file. If not
  provided, capital letters will be used as labels in the report.
• exp_type: A character vector of experimental types for each peak
  file.
  Useful for comparison of different methods. If not provided, all
  datasets will be classified as “unknown” experiment types in the
  report. exp_type is used only for labelling. It does not affect the
  analyses. You can also input custom strings. Datasets will be grouped
  as long as they match their respective exp_type. Supported
  experimental types are:
  • chipseq: ChIP-seq data
  • tipseq: TIP-seq data
  • cuttag: CUT&Tag data
  • cutrun: CUT&Run data
• motif_files: A character vector of path to motif files, or a vector
  of universalmotif-class objects. Required to run Known Motif
  Enrichment Analysis. JASPAR matrix IDs can also be provided to
  automatically fetch motifs from the JASPAR.
• motif_labels: A character vector of labels for each motif file. Only
  used if path to file names are passed in motif_files. If not provided,
  the motif file names will be used as labels.
• cell_counts: An integer vector of experiment cell counts for each
  peak file (if available). Creates additional comparisons based on cell
  counts.
• motif_db: Path to .meme format file to use as reference database,
  or a list of universalmotif-class objects. Results from motif
  discovery are searched against this database to find similar motifs.
  If not provided, JASPAR CORE database will be used, making this
  parameter truly optional. NOTE: p-value estimates are
  inaccurate when the database has fewer than 50 entries.

• BPPARAM = MulticoreParam(x): Running motif discovery in parallel can
  significantly reduce runtime, but it is very memory-intensive,
  consuming upwards of 10GB of RAM per thread. Memory starvation can
  greatly slow the process, so set CPU cores (x) with caution.
• motif_discovery_count: The number of motifs to discover per sequence
  group exponentially increases runtime. We recommend no more than 5
  motifs to make a meaningful inference.
• trim_seq_width: Trimming sequences before running motif discovery
  can significantly reduce the search space. Sequence length can
  exponentially increase runtime. We recommend running the script with
  motif_discovery = FALSE and studying the motif-summit distance
  distribution under general metrics to find the sequence length that
  captures most motifs. A good starting point is 150 but it can be
  reduced further if appropriate.

• CTCF_TIP_peaks: Human CTCF peak file generated with TIP-seq using
  HCT116 cell-line. No control files were used to generate the peak
  file. The peaks were called using MACS3 with
  CTCF_TIP_alignment.bam as input.
• CTCF_ChIP_peaks: Human CTCF peak file generated with ChIP-seq using
  HCT116 cell-line. No control files were used to generate the peak
  file. The peaks were called using MACS3 with
  CTCF_ChIP_alignment.bam as input.
• motif_MA1102.3: The JASPAR motif for CTCFL (MA1102.3) for Homo
  Sapiens. Sourced from
  JASPAR
• motif_MA1930.2: The JASPAR motif for CTCFL (MA1930.2) for Homo
  Sapiens. Sourced from
  JASPAR
• CTCF_TIP_alignment.bam: Human CTCF alignment file generated with
  TIP-seq using HCT116 cell-line. The alignment file was generated using
  the nf-core/cutandrun pipeline.
  Raw read files were sourced from NIH Sequence Read Archives ID:
  SRR16963166.
  Only available as extdata.
• CTCF_ChIP_alignment.bam: Human CTCF alignment file generated with
  ChIP-seq using HCT116 cell-line. Sourced from ENCODE (Accession:
  ENCFF091ODJ). Only
  available as extdata.

utils::sessionInfo()

## R Under development (unstable) (2025-10-27 r88972)
## Platform: aarch64-apple-darwin20
## Running under: macOS Tahoe 26.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/London
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        jsonlite_2.0.0      renv_1.1.5         
##  [4] dplyr_1.1.4         compiler_4.6.0      BiocManager_1.30.26
##  [7] tidyselect_1.2.1    rvcheck_0.2.1       scales_1.4.0       
## [10] yaml_2.3.10         fastmap_1.2.0       here_1.0.2         
## [13] ggplot2_4.0.0       R6_2.6.1            generics_0.1.4     
## [16] knitr_1.50          yulab.utils_0.2.1   tibble_3.3.0       
## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.1.1    
## [22] pillar_1.11.1       RColorBrewer_1.1-3  rlang_1.1.6        
## [25] badger_0.2.5        xfun_0.54           fs_1.6.6           
## [28] S7_0.2.0            cli_3.6.5           magrittr_2.0.4     
## [31] rworkflows_1.0.6    digest_0.6.37       grid_4.6.0         
## [34] rstudioapi_0.17.1   rappdirs_0.3.3      lifecycle_1.0.4    
## [37] vctrs_0.6.5         evaluate_1.0.5      glue_1.8.0         
## [40] data.table_1.17.8   farver_2.1.2        rmarkdown_2.30     
## [43] tools_4.6.0         pkgconfig_2.0.3     htmltools_0.5.8.1