Spencer Nystrom

I've just run into an annoying issue building on a system where I lack `sudo`. While compiling locally with `cross` is possible for me, it would be great if folks...

Implements strandedness for filter_by_overlap() family. Closes #96.

1

I added a set of `_directed()` methods for the `filter_by_overlap` family: `filter_by_overlaps_directed()` and `filter_by_non_overlaps_directed()`. This family of methods was also missing some unit tests so I added a few for...

Coltypes are inconsistent if blast returns no hits

1

Data import step should be changed to always read in each column as the same data type. When an empty data.frame is read by read.table all columns default to `lgl`...

The goal of this visualization is to draw a rectangular box spanning facet boundaries for the purpose of highlighting a range of data along a continuous scale. I think this...

enrichPathway make readable does not work for yeast genome

7

Issue stems from enrichPathway looking for a column named SYMBOL which does not exist in the org.Sc.sgd.db object (see `columns(org.Sc.sgd.db)`). Instead for yeast this should use the "GENENAME" column. Alternately,...

Option to deprotect `motif` column in universalmotif_df

3

I was just messing around with a set of motifs and I wanted to selectively RC one while using a universalmotif_df. ``` df % mutate(motif = ifelse(name == "motif2", motif_rc(motif),...

Solution: ``` x % cmd_ui_file_exists(), silent = TRUE) if (class(x) == "try-error") { # if block below is the addition, make the message a little nicer, but this is the...

cmd_is_installed fails if no utils defined

1

Because cmd_is_installed calls `util = TRUE`, if no utils, get error. This really highlights how this is a bad design choice to begin with #22. ``` my_fun

See `snystrom/memes #65`

expose cmd_list_keep/drop internals

1

These are useful helpers for a specific case when something is named. `cmd_list_drop/keep` is a useful helper when case is generic, but specificity can be good sometimes. In fact, I...