motifmatchr
motifmatchr copied to clipboard
GreenleafLab
Fast motif matching in R
I am trying get motifs positions within ATAC-Seq peaks: `motif_ranges sessionInfo() R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Rocky Linux 9.1 (Blue Onyx) Matrix products: default BLAS/LAPACK: /home/kurowsaa/miniconda3/envs/chromVAR_env/lib/libopenblasp-r0.3.26.so;...
motifmatchr fails when using some motifs collections (e.g. https://doi.org/10.1093/nar/gkad1240 ) due to small rounding errors in the column sums of the PFM preventing `pwmType` from determining whether the motifs are...
Hi I have a question. When I execute the `matchMotifs` function, an error appears: Error in loadFUN(x, seqname, ranges): trying to load regions beyond the boundaries of non-circular sequence "chr3"...
Hello, I just wanted to check and see if motifmatchr considers the reverse compliment when matching motifs? I assume that this is the case but wanted to check. (This probably...
when using the motifMatches() to scan the sequence in chromVAR , I awalys use JASPAR2016/JASPAR2018 to get the PFMatrix. But the number of motif in database is limited. And some...
Apologies, wasn't sure if this was the best place to post, but: 1. Is there a way of extracting a column of p-values along with the positions? 2. Is there...
in vignette on pkgdown site, an issue with ``` motif_ix_BSgenomeViews
Hello author, Thank you for providing the great tool! I have a question about matchMotifs() results. When I run the function with the different sets of GRanges (as the second...
