How to combine a data frame with another data frame containing comma-separated values?

For dataframe manipulation, in general, you should look into the dplyr and tidyr packages, they offer endless possibilities if you learn to manipulate them (lots of practice will help). A good and concise cheatsheet is available here.

Regarding this problem in particular, something like this should work:

library(dplyr)
library(tidyr)

dfA <- data.frame(gene = c("a", "b", "c", "d", "e"),
                  mus_id = c("mus001", "mus002", "mus003", "mus004", "mus005"))

dfB <- data.frame(mus_id = c("mus001", "mus002", "mus003,mus002", "mus004"),
                  zeb_id = c("dar001", "dar002,dar004", "dar003,dar002", "dar004"))

dfC <-  dfB %>%
  tidyr::separate_rows(zeb_id, sep = ",") %>%
  tidyr::separate_rows(mus_id, sep = ",") %>%
  dplyr::group_by(mus_id) %>%
  dplyr::summarise(zeb_id = paste0(sort(unique(na.omit(zeb_id))), collapse=","))

dfD <- dfA %>%
  dplyr::left_join(dfC)