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fastqcr 0.1.3

Minor changes

• Using select() in place of the deprecated select_() function in qc_aggregate() and qc_problems() (#24)
• Using arrange() and group_by() in place of the deprecated arrange_() and group_by()_ functions in qc_problems()
• Changing http to https for urls concerning fastc installation and documentation
• qc_read_collection() and qc_plot_collection() examples reduced to less than 5 seconds

Bug fixes

• Remove extra args (fill) in left_join() from qc_aggregate() function (#23)

fastqcr 0.1.2

Bug fixes

• Revert “Fix for readr 1.2.0”: readr 1.3.0 changes the skip line behavior to match that of readr 1.1.1, the change in 1.2.0 was determined to be too disruptive (@jimhester, #11).

fastqcr 0.1.1

New features

New functions added to read and plot a collection of samples together:

• qc_read_collection() (@MahShaaban , #4)
• qc_plot_collection() (@MahShaaban , #4)

When possible, the data from multiple samples are overlayed on a single graph and otherwise on multiple facets (when there is more than one line in a one sample plot). As with plotting the single file modules, the function qc_plot_collection() dispatches on the appropriate class qc_read_collection() and calls the internals corresponding to the input of the argument modules.

Bug fixes

• Fix for readr 1.2.0 (@jimhester, #7)

Minor changes

• New argument fastqc.path added to the function fastqc().

Bug fixes

fastqcr 0.1.0

Bug fixes

• Now, qc_report() handles better relative paths to FastQC zipfiles (@ACharbonneau, #1)

New features

• fastqc_install(): Install the latest version of FastQC tool on Unix systems (MAC OSX and Linux)

• fastqc(): Run the FastQC tool from R.

• qc <- qc_aggregate(): Aggregate multiple FastQC reports into a data frame.

• summary(qc): Generates a summary of qc_aggregate.

• qc_stats(qc): General statistics of FastQC reports.

• qc_fails(qc): Displays samples or modules that failed.

• qc_warns(qc): Displays samples or modules that warned.

• qc_problems(qc, “sample”): Union of qc_fails() and qc_warns(). Display which samples or modules that failed or warned.

• qc_read(): Read FastQC data into R.

• qc_plot(qc): Plot FastQC data

• qc_report(): Create an HTML file containing FastQC reports of one or multiple files. Inputs can be either a directory containing multiple FastQC reports or a single sample FastQC report.

• qc_unzip(): Unzip all zipped files in the qc.dir directory.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.