i) added man pages for the new functions
ii) updated user guide with examples of ccr.FASTQ2counts and ccr.AnalysisPipeline
iii) minor fixes in the pipeline function to accept relative paths for all input files
iii) minor fixes in the order of the input parameters in the new functions
iv) added direct reference (::) to the withr package functions
i) added man pages for the new functions ii) updated user guide with examples of ccr.FASTQ2counts and ccr.AnalysisPipeline iii) minor fixes in the pipeline function to accept relative paths for all input files iii) minor fixes in the order of the input parameters in the new functions iv) added direct reference (::) to the withr package functions