marge 0.0.4.9999

contributed by @mperalc : added read_denovo_html_results() to extract information from matched known motifs related to the de novo found motifs ("similar motifs found" under "best match/details") - see denovo motif html output for example

marge 0.0.4

added more information regarding installation hiccups and finding HOMER
migrating to Github for long-term, removing references to Bitbucket
removed requirement to filter by log odds detection greater than 0 when appending known pwms in utils.R

completely reworked how marge checks for HOMER installation -
- Uses options('homer_path') to hold the installation base path
- Tries the default (e.g. if HOMER is a part of $PATH) first, susses out HOMER base
- Failing that, asks for user to manually set it, and provides code to set in .Rprofile
- Instructions encoded into messages following success/failure
added an onAttach.R to check for proper HOMER install on load with link to online docs

bug fix for find_motifs_genome when using a custom background - added an fdr_num argument to add number of iterations for FDR calculation (background file was being fed to -fdr as the <num> argument); set to 0 by default since runtime takes forever when set when doing denovo enrichment
reads in new fdr field for denovo results, as the fdr arg for find_motifs_genome has now been enabled by default always
bug fix for find_motifs_genome - motif_length arg was only using the first number
added find_motifs_instances function to get where specific motifs (based on PWM) occur in peaks
added write_pwm function to support find_motifs_instances
created new datafile HOMER_motifs which includes all motifs used by HOMER - includes their PWMs, organism/motif set definition info
removed placeholder functions [read|write]_bed that were initially included for testing
added a new vignette

initial release of marge which includes the most basic utilities needed for analysis (see below)
find_motifs_genome - runs motif analysis using HOMER; creates a HOMER results directory
read_denovo_results - reads the homerMotifs.all.motifs file created in the HOMER results directory
read_known_results - reads the knownResults.txt file created in the HOMER results directory