memes
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snystrom
An R interface to the MEME Suite
Hi, I have installed successfully memes under my Rstudio server that runs under a WSL2 interfaced Ubuntu, and processed many sequences by ame and FIMO without any problem. I however...
I installed meme with macports on a mac The program is in /opt/local/share/meme-5.5.0. I used this in R options(meme_bin = "/opt/local/share/meme-5.5.0") when I check_meme_install there is a green check mark...
data viz
- [ ] visualization for occurance along linear feature (ex indicating position of motifs along multiple proteins) - using relative position to start site coords (ie 1 -> N) ##...
Didn't have time to do this when fixing #90, but currently `importStremeXML()` is untested.
From release notes: ``` Added the motif alternate ID to the sequence.tsv output. The new column in the TSV file is named "motif_ALT_ID". ```
plot histogram of sequence lengths for BSlist, etc. to check length distribution assumptions for meme/streme? May be kind of useful for some folks who don't do size cutoffs.
using a lexical sort for `plot_sequence_heatmap` could be one way to improve the visualization. However, a naive lexical sort won't capture the "core" of a motif correctly, and will make...
Example: ``` m
## Issue Current unit tests are in bad shape & need formalization. ### Ame - [ ] import each data type (fisher, dhmg, etc) ### TomTom - [ ] add...
MEME suite can't run on windows, so good idea to error informatively. **Tests to write** - error when OS == windows