# MACSr

#### 9 May 2023

# 1 Introduction

With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we presented the Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity. Moreover, as a general peak-caller, MACS can also be applied to any “DNA enrichment assays” if the question to be asked is simply: where we can find significant reads coverage than the random background.

This package is a wrapper of the MACS toolkit based on `basilisk`.

# 2 Load the package

The package is built on basilisk. The dependent python library macs3 will be installed automatically inside its conda environment.

    library(MACSr)

# 3 Usage

## 3.1 MACS3 functions

There are 13 functions imported from MACS3. Details of each function can be checked from its manual.

Functions | Description
--- | ---
`callpeak` | Main MACS3 Function to call peaks from alignment results.
`bdgpeakcall` | Call peaks from bedGraph output.
`bdgbroadcall` | Call broad peaks from bedGraph output.
`bdgcmp` | Comparing two signal tracks in bedGraph format.
`bdgopt` | Operate the score column of bedGraph file.
`cmbreps` | Combine BEDGraphs of scores from replicates.
`bdgdiff` | Differential peak detection based on paired four bedGraph files.
`filterdup` | Remove duplicate reads, then save in BED/BEDPE format.
`predictd` | Predict d or fragment size from alignment results.
`pileup` | Pileup aligned reads (single-end) or fragments (paired-end)
`randsample` | Randomly choose a number/percentage of total reads.
`refinepeak` | Take raw reads alignment, refine peak summits.
`callvar` | Call variants in given peak regions from the alignment BAM files.

## 3.2 Function `callpeak`

We have uploaded multipe test datasets from MACS to a data package `MACSdata` in the `ExperimentHub`. For example, Here we download a pair of single-end bed files to run the `callpeak` function.

    eh <- ExperimentHub::ExperimentHub()
    eh <- AnnotationHub::query(eh, "MACSdata")
    CHIP <- eh[["EH4558"]]
    #> see ?MACSdata and browseVignettes('MACSdata') for documentation
    #> loading from cache
    CTRL <- eh[["EH4563"]]
    #> see ?MACSdata and browseVignettes('MACSdata') for documentation
    #> loading from cache

Here is an example to call narrow and broad peaks on the SE bed files.

    cp1 <- callpeak(CHIP, CTRL, gsize = 5.2e7, store_bdg = TRUE,
                    name = "run_callpeak_narrow0", outdir = tempdir(),
                    cutoff_analysis = TRUE)
    #> INFO  @ Tue, 09 May 2023 05:59:23:
    #> # Command line:
    #> # ARGUMENTS LIST:
    #> # name = run_callpeak_narrow0
    #> # format = AUTO
    #> # ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e97067e67289_4601']
    #> # control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e9704a69b5a9_4606']
    #> # effective genome size = 5.20e+07
    #> # band width = 300
    #> # model fold = [5.0, 50.0]
    #> # qvalue cutoff = 5.00e-02
    #> # The maximum gap between significant sites is assigned as the read length/tag size.
    #> # The minimum length of peaks is assigned as the predicted fragment length "d".
    #> # Larger dataset will be scaled towards smaller dataset.
    #> # Range for calculating regional lambda is: 1000 bps and 10000 bps
    #> # Broad region calling is off
    #> # Additional cutoff on fold-enrichment is: 0.10
    #> # Paired-End mode is off
    #>
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 read tag files...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 read treatment tags...
    #> INFO  @ Tue, 09 May 2023 05:59:23: Detected format is: BED
    #> INFO  @ Tue, 09 May 2023 05:59:23: * Input file is gzipped.
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1.2 read input tags...
    #> INFO  @ Tue, 09 May 2023 05:59:23: Detected format is: BED
    #> INFO  @ Tue, 09 May 2023 05:59:23: * Input file is gzipped.
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 tag size is determined as 101 bps
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 tag size = 101.0
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1  total tags in treatment: 49622
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 user defined the maximum tags...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1  tags after filtering in treatment: 48047
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1  Redundant rate of treatment: 0.03
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1  total tags in control: 50837
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 user defined the maximum tags...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1  tags after filtering in control: 50783
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1  Redundant rate of control: 0.00
    #> INFO  @ Tue, 09 May 2023 05:59:23: #1 finished!
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 Build Peak Model...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 looking for paired plus/minus strand peaks...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 Total number of paired peaks: 469
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 Model building with cross-correlation: Done
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 finished!
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 predicted fragment length is 228 bps
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2 alternative fragment length(s) may be 228 bps
    #> INFO  @ Tue, 09 May 2023 05:59:23: #2.2 Generate R script for model : /tmp/RtmpcbjxsB/run_callpeak_narrow0_model.r
    #> INFO  @ Tue, 09 May 2023 05:59:23: #3 Call peaks...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #3 Pre-compute pvalue-qvalue table...
    #> INFO  @ Tue, 09 May 2023 05:59:23: #3 Cutoff vs peaks called will be analyzed!
    #> INFO  @ Tue, 09 May 2023 05:59:24: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpcbjxsB/run_callpeak_narrow0_cutoff_analysis.txt'
    #> INFO  @ Tue, 09 May 2023 05:59:24: #3 In the peak calling step, the following will be performed simultaneously:
    #> INFO  @ Tue, 09 May 2023 05:59:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg
    #> INFO  @ Tue, 09 May 2023 05:59:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg
    #> INFO  @ Tue, 09 May 2023 05:59:24: #3   Pileup will be based on sequencing depth in treatment.
    #> INFO  @ Tue, 09 May 2023 05:59:24: #3 Call peaks for each chromosome...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #4 Write output xls file... /tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.xls
    #> INFO  @ Tue, 09 May 2023 05:59:25: #4 Write peak in narrowPeak format file... /tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.narrowPeak
    #> INFO  @ Tue, 09 May 2023 05:59:25: #4 Write summits bed file... /tmp/RtmpcbjxsB/run_callpeak_narrow0_summits.bed
    #> INFO  @ Tue, 09 May 2023 05:59:25: Done!
    cp2 <- callpeak(CHIP, CTRL, gsize = 5.2e7, store_bdg = TRUE,
                    name = "run_callpeak_broad", outdir = tempdir(),
                    broad = TRUE)
    #> INFO  @ Tue, 09 May 2023 05:59:25:
    #> # Command line:
    #> # ARGUMENTS LIST:
    #> # name = run_callpeak_broad
    #> # format = AUTO
    #> # ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e97067e67289_4601']
    #> # control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e9704a69b5a9_4606']
    #> # effective genome size = 5.20e+07
    #> # band width = 300
    #> # model fold = [5.0, 50.0]
    #> # qvalue cutoff for narrow/strong regions = 5.00e-02
    #> # qvalue cutoff for broad/weak regions = 1.00e-01
    #> # The maximum gap between significant sites is assigned as the read length/tag size.
    #> # The minimum length of peaks is assigned as the predicted fragment length "d".
    #> # Larger dataset will be scaled towards smaller dataset.
    #> # Range for calculating regional lambda is: 1000 bps and 10000 bps
    #> # Broad region calling is on
    #> # Additional cutoff on fold-enrichment is: 0.10
    #> # Paired-End mode is off
    #>
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 read tag files...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 read treatment tags...
    #> INFO  @ Tue, 09 May 2023 05:59:25: Detected format is: BED
    #> INFO  @ Tue, 09 May 2023 05:59:25: * Input file is gzipped.
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1.2 read input tags...
    #> INFO  @ Tue, 09 May 2023 05:59:25: Detected format is: BED
    #> INFO  @ Tue, 09 May 2023 05:59:25: * Input file is gzipped.
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 tag size is determined as 101 bps
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 tag size = 101.0
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1  total tags in treatment: 49622
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 user defined the maximum tags...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1  tags after filtering in treatment: 48047
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1  Redundant rate of treatment: 0.03
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1  total tags in control: 50837
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 user defined the maximum tags...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1  tags after filtering in control: 50783
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1  Redundant rate of control: 0.00
    #> INFO  @ Tue, 09 May 2023 05:59:25: #1 finished!
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 Build Peak Model...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 looking for paired plus/minus strand peaks...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 Total number of paired peaks: 469
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 Model building with cross-correlation: Done
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 finished!
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 predicted fragment length is 228 bps
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2 alternative fragment length(s) may be 228 bps
    #> INFO  @ Tue, 09 May 2023 05:59:25: #2.2 Generate R script for model : /tmp/RtmpcbjxsB/run_callpeak_broad_model.r
    #> INFO  @ Tue, 09 May 2023 05:59:25: #3 Call peaks...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #3 Call broad peaks with given level1 -log10qvalue cutoff and level2: 1.301030, 1.000000...
    #> INFO  @ Tue, 09 May 2023 05:59:25: #3 Pre-compute pvalue-qvalue table...
    #> INFO  @ Tue, 09 May 2023 05:59:26: #3 In the peak calling step, the following will be performed simultaneously:
    #> INFO  @ Tue, 09 May 2023 05:59:26: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_broad_treat_pileup.bdg
    #> INFO  @ Tue, 09 May 2023 05:59:26: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_broad_control_lambda.bdg
    #> INFO  @ Tue, 09 May 2023 05:59:26: #3 Call peaks for each chromosome...
    #> INFO  @ Tue, 09 May 2023 05:59:26: #4 Write output xls file... /tmp/RtmpcbjxsB/run_callpeak_broad_peaks.xls
    #> INFO  @ Tue, 09 May 2023 05:59:26: #4 Write broad peak in broadPeak format file... /tmp/RtmpcbjxsB/run_callpeak_broad_peaks.broadPeak
    #> INFO  @ Tue, 09 May 2023 05:59:26: #4 Write broad peak in bed12/gappedPeak format file... /tmp/RtmpcbjxsB/run_callpeak_broad_peaks.gappedPeak
    #> INFO  @ Tue, 09 May 2023 05:59:26: Done!

Here are the outputs.

    cp1
    #> macsList class
    #> $outputs:
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_control_lambda.bdg
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_cutoff_analysis.txt
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_model.r
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.narrowPeak
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.xls
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_summits.bed
    #>  /tmp/RtmpcbjxsB/run_callpeak_narrow0_treat_pileup.bdg
    #> $arguments: tfile, cfile, gsize, outdir, name, store_bdg, cutoff_analysis
    #> $log:
    #>  INFO  @ Tue, 09 May 2023 05:59:23:
    #>  # Command line:
    #>  # ARGUMENTS LIST:
    #>  # name = run_callpeak_narrow0
    #>  # format = AUTO
    #> ...
    cp2
    #> macsList class
    #> $outputs:
    #>  /tmp/RtmpcbjxsB/run_callpeak_broad_control_lambda.bdg
    #>  /tmp/RtmpcbjxsB/run_callpeak_broad_model.r
    #>  /tmp/RtmpcbjxsB/run_callpeak_broad_peaks.broadPeak
    #>  /tmp/RtmpcbjxsB/run_callpeak_broad_peaks.gappedPeak
    #>  /tmp/RtmpcbjxsB/run_callpeak_broad_peaks.xls
    #>  /tmp/RtmpcbjxsB/run_callpeak_broad_treat_pileup.bdg
    #> $arguments: tfile, cfile, gsize, outdir, name, store_bdg, broad
    #> $log:
    #>  INFO  @ Tue, 09 May 2023 05:59:25:
    #>  # Command line:
    #>  # ARGUMENTS LIST:
    #>  # name = run_callpeak_broad
    #>  # format = AUTO
    #> ...

## 3.3 The `macsList` class

The `macsList` is designed to contain everything of an execution, including function, inputs, outputs and logs, for the purpose of reproducibility.

For example, we can the function and input arguments.

    cp1$arguments
    #> [[1]]
    #> callpeak
    #>
    #> $tfile
    #> CHIP
    #>
    #> $cfile
    #> CTRL
    #>
    #> $gsize
    #> [1] 5.2e+07
    #>
    #> $outdir
    #> tempdir()
    #>
    #> $name
    #> [1] "run_callpeak_narrow0"
    #>
    #> $store_bdg
    #> [1] TRUE
    #>
    #> $cutoff_analysis
    #> [1] TRUE

The files of all the outputs are collected.

    cp1$outputs
    #> [1] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_control_lambda.bdg"
    #> [2] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_cutoff_analysis.txt"
    #> [3] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_model.r"
    #> [4] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.narrowPeak"
    #> [5] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.xls"
    #> [6] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_summits.bed"
    #> [7] "/tmp/RtmpcbjxsB/run_callpeak_narrow0_treat_pileup.bdg"

The `log` is especially important for `MACS` to check. Detailed information was given in the log when running.

    cat(cp1$log)
    #> INFO  @ Tue, 09 May 2023 05:59:23:  # Command line:  # ARGUMENTS LIST: # name = run_callpeak_narrow0 # format = AUTO # ChIP-seq file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e97067e67289_4601'] # control file = ['/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/e9704a69b5a9_4606'] # effective genome size = 5.20e+07 # band width = 300 # model fold = [5.0, 50.0] # qvalue cutoff = 5.00e-02 # The maximum gap between significant sites is assigned as the read length/tag size. # The minimum length of peaks is assigned as the predicted fragment length "d". # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is off # Additional cutoff on fold-enrichment is: 0.10 # Paired-End mode is off   INFO  @ Tue, 09 May 2023 05:59:23: #1 read tag files...  INFO  @ Tue, 09 May 2023 05:59:23: #1 read treatment tags...  INFO  @ Tue, 09 May 2023 05:59:23: Detected format is: BED  INFO  @ Tue, 09 May 2023 05:59:23: * Input file is gzipped.  INFO  @ Tue, 09 May 2023 05:59:23: #1.2 read input tags...  INFO  @ Tue, 09 May 2023 05:59:23: Detected format is: BED  INFO  @ Tue, 09 May 2023 05:59:23: * Input file is gzipped.  INFO  @ Tue, 09 May 2023 05:59:23: #1 tag size is determined as 101 bps  INFO  @ Tue, 09 May 2023 05:59:23: #1 tag size = 101.0  INFO  @ Tue, 09 May 2023 05:59:23: #1  total tags in treatment: 49622  INFO  @ Tue, 09 May 2023 05:59:23: #1 user defined the maximum tags...  INFO  @ Tue, 09 May 2023 05:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)  INFO  @ Tue, 09 May 2023 05:59:23: #1  tags after filtering in treatment: 48047  INFO  @ Tue, 09 May 2023 05:59:23: #1  Redundant rate of treatment: 0.03  INFO  @ Tue, 09 May 2023 05:59:23: #1  total tags in control: 50837  INFO  @ Tue, 09 May 2023 05:59:23: #1 user defined the maximum tags...  INFO  @ Tue, 09 May 2023 05:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)  INFO  @ Tue, 09 May 2023 05:59:23: #1  tags after filtering in control: 50783  INFO  @ Tue, 09 May 2023 05:59:23: #1  Redundant rate of control: 0.00  INFO  @ Tue, 09 May 2023 05:59:23: #1 finished!  INFO  @ Tue, 09 May 2023 05:59:23: #2 Build Peak Model...  INFO  @ Tue, 09 May 2023 05:59:23: #2 looking for paired plus/minus strand peaks...  INFO  @ Tue, 09 May 2023 05:59:23: #2 Total number of paired peaks: 469  INFO  @ Tue, 09 May 2023 05:59:23: #2 Model building with cross-correlation: Done  INFO  @ Tue, 09 May 2023 05:59:23: #2 finished!  INFO  @ Tue, 09 May 2023 05:59:23: #2 predicted fragment length is 228 bps  INFO  @ Tue, 09 May 2023 05:59:23: #2 alternative fragment length(s) may be 228 bps  INFO  @ Tue, 09 May 2023 05:59:23: #2.2 Generate R script for model : /tmp/RtmpcbjxsB/run_callpeak_narrow0_model.r  INFO  @ Tue, 09 May 2023 05:59:23: #3 Call peaks...  INFO  @ Tue, 09 May 2023 05:59:23: #3 Pre-compute pvalue-qvalue table...  INFO  @ Tue, 09 May 2023 05:59:23: #3 Cutoff vs peaks called will be analyzed!  INFO  @ Tue, 09 May 2023 05:59:24: #3 Analysis of cutoff vs num of peaks or total length has been saved in b'/tmp/RtmpcbjxsB/run_callpeak_narrow0_cutoff_analysis.txt'  INFO  @ Tue, 09 May 2023 05:59:24: #3 In the peak calling step, the following will be performed simultaneously:  INFO  @ Tue, 09 May 2023 05:59:24: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... run_callpeak_narrow0_treat_pileup.bdg  INFO  @ Tue, 09 May 2023 05:59:24: #3   Write bedGraph files for control lambda (after scaling if necessary)... run_callpeak_narrow0_control_lambda.bdg  INFO  @ Tue, 09 May 2023 05:59:24: #3   Pileup will be based on sequencing depth in treatment.  INFO  @ Tue, 09 May 2023 05:59:24: #3 Call peaks for each chromosome...  INFO  @ Tue, 09 May 2023 05:59:25: #4 Write output xls file... /tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.xls  INFO  @ Tue, 09 May 2023 05:59:25: #4 Write peak in narrowPeak format file... /tmp/RtmpcbjxsB/run_callpeak_narrow0_peaks.narrowPeak  INFO  @ Tue, 09 May 2023 05:59:25: #4 Write summits bed file... /tmp/RtmpcbjxsB/run_callpeak_narrow0_summits.bed  INFO  @ Tue, 09 May 2023 05:59:25: Done!

# 4 Resources

More details about `MACS3` can be found: https://macs3-project.github.io/MACS/.

# 5 SessionInfo

    sessionInfo()
    #> R version 4.3.0 RC (2023-04-13 r84266)
    #> Platform: aarch64-apple-darwin20 (64-bit)
    #> Running under: macOS Monterey 12.6.1
    #>
    #> Matrix products: default
    #> BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
    #>
    #> locale:
    #> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    #>
    #> time zone: America/New_York
    #> tzcode source: internal
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> other attached packages:
    #> [1] MACSdata_1.7.0   MACSr_1.8.0      BiocStyle_2.28.0
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] KEGGREST_1.40.0               dir.expiry_1.8.0
    #>  [3] xfun_0.38                     bslib_0.4.2
    #>  [5] Biobase_2.60.0                lattice_0.21-8
    #>  [7] bitops_1.0-7                  vctrs_0.6.1
    #>  [9] tools_4.3.0                   generics_0.1.3
    #> [11] stats4_4.3.0                  curl_5.0.0
    #> [13] parallel_4.3.0                tibble_3.2.1
    #> [15] fansi_1.0.4                   AnnotationDbi_1.62.1
    #> [17] RSQLite_2.3.1                 blob_1.2.4
    #> [19] pkgconfig_2.0.3               Matrix_1.5-4
    #> [21] dbplyr_2.3.2                  S4Vectors_0.38.1
    #> [23] GenomeInfoDbData_1.2.10       lifecycle_1.0.3
    #> [25] compiler_4.3.0                Biostrings_2.68.0
    #> [27] GenomeInfoDb_1.36.0           httpuv_1.6.9
    #> [29] htmltools_0.5.5               sass_0.4.5
    #> [31] RCurl_1.98-1.12               yaml_2.3.7
    #> [33] interactiveDisplayBase_1.38.0 crayon_1.5.2
    #> [35] pillar_1.9.0                  later_1.3.0
    #> [37] jquerylib_0.1.4               ellipsis_0.3.2
    #> [39] cachem_1.0.7                  mime_0.12
    #> [41] ExperimentHub_2.8.0           AnnotationHub_3.8.0
    #> [43] basilisk_1.12.0               tidyselect_1.2.0
    #> [45] digest_0.6.31                 purrr_1.0.1
    #> [47] dplyr_1.1.1                   bookdown_0.33
    #> [49] BiocVersion_3.17.1            rprojroot_2.0.3
    #> [51] fastmap_1.1.1                 grid_4.3.0
    #> [53] here_1.0.1                    cli_3.6.1
    #> [55] magrittr_2.0.3                utf8_1.2.3
    #> [57] withr_2.5.0                   filelock_1.0.2
    #> [59] promises_1.2.0.1              rappdirs_0.3.3
    #> [61] bit64_4.0.5                   XVector_0.40.0
    #> [63] rmarkdown_2.21                httr_1.4.5
    #> [65] bit_4.0.5                     reticulate_1.28
    #> [67] png_0.1-8                     memoise_2.0.1
    #> [69] shiny_1.7.4                   evaluate_0.20
    #> [71] knitr_1.42                    IRanges_2.34.0
    #> [73] basilisk.utils_1.12.0         BiocFileCache_2.8.0
    #> [75] rlang_1.1.0                   Rcpp_1.0.10
    #> [77] xtable_1.8-4                  glue_1.6.2
    #> [79] DBI_1.1.3                     BiocManager_1.30.20
    #> [81] BiocGenerics_0.46.0           jsonlite_1.8.4
    #> [83] R6_2.5.1                      zlibbioc_1.46.0