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Example Reports

Source: vignettes/articles/examples.Rmd
examples.Rmd

Updated: Nov-12-2024

MotifPeeker-reports is a public archive for interactive HTML reports generated by MotifPeeker, along with the code used to produce them.

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CTCF ChIP-seq - TIP-seq

Dataset Details

Compares three public ChIP-seq datasets against a TIP-seq dataset for CTCF in HCT116 cells. Details of the datasets used are as follows:

  1. ChIPSeq1
    ENCODE Accession: ENCFF172XLC
  2. ChIPSeq2
    ENCODE Accession: ENCFF411OOS
  3. ChIPSeq3
    ENCODE Accession: ENCFF091ODJ
  4. TIPSeq
    Alignment file produced by running the nf-core/cutandrun pipeline on the raw sequencing data sourced from NIH Sequence Read Archives ID: SRR16963166.

Peak calling was performed using MACS3 using the following commands:

## For ChIP-Seq datasets
MACSr::callpeak(
        tfile = ...,
        cfile = NULL,  # No control file
        nomodel = FALSE,
        qvalue = 0.01,
        format = "BAM",
        name = "chipseq",
        outdir = ...
    )
    
## For TIP-Seq dataset
MACSr::callpeak(
        tfile = tipseq_alignment_data,
        nomodel = TRUE,
        qvalue = 0.01,
        shift = -75,  # 5' shift
        extsize = 150,
        keepduplicates = "all",
        format = "BAM",
        name = "tipseq",
        outdir = ...
    )

Motif files used:

  1. CTCF motif MA1930.2
  2. CTCFL motif MA1102.3

 Code

Built-in data

Dataset Details Report generated from built-in data, as described in the MotifPeeker vignette.

 Code

Session Info 

utils::sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     desc_1.4.3        R6_2.5.1          fastmap_1.2.0    
##  [5] xfun_0.49         cachem_1.1.0      knitr_1.49        htmltools_0.5.8.1
##  [9] rmarkdown_2.29    lifecycle_1.0.4   cli_3.6.3         sass_0.4.9       
## [13] pkgdown_2.1.1     textshaping_0.4.0 jquerylib_0.1.4   systemfonts_1.1.0
## [17] compiler_4.4.1    tools_4.4.1       ragg_1.3.2        bslib_0.8.0      
## [21] evaluate_1.0.1    yaml_2.3.10       jsonlite_1.8.9    rlang_1.1.4      
## [25] fs_1.6.5          htmlwidgets_1.6.4