Package: memes 1.13.0

Spencer Nystrom

memes: motif matching, comparison, and de novo discovery using the MEME Suite

A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.

Authors:Spencer Nystrom [aut, cre, cph]

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memes.pdf |memes.html✨
memes/json (API)
NEWS

# Install 'memes' in R:
install.packages('memes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/snystrom/memes/issues

Datasets:

On BioConductor:memes-1.13.0(bioc 3.20)memes-1.12.0(bioc 3.19)

bioconductor-package

27 exports 0.49 score 103 dependencies 1 mentions

Last updated 2 months agofrom:10e69e61df

Exports:add_sequenceame_compare_heatmap_methodscheck_meme_installdrop_best_matchforce_best_matchget_sequencehas_duplicate_motifsimportAmeimportDremeXMLimportFimoimportMemeimportStremeXMLimportTomTomXMLmeme_is_installednest_tomtomplot_ame_heatmapplot_sequence_heatmapremove_duplicate_motifsrunAmerunDremerunFimorunMemerunStremerunTomTomupdate_best_matchview_tomtom_hitswrite_fasta

Dependencies:askpassBiocGenericsBiostringsbitbit64briocallrclicliprcmdfuncolorspacecpp11crayoncredentialscurldescdiffobjdigestdplyrevaluatefansifarverfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgertggplot2ggseqlogoghgitcredsgluegtablehmshttrhttr2iniIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppThreadreadrrematch2rlangrprojrootrstudioapiS4VectorsscalesstringistringrsystestthattibbletidyrtidyselecttzdbUCSC.utilsuniversalmotifusethisutf8vctrsviridisLitevroomwaldowhiskerwithrxml2XVectoryamlzipzlibbioc

ChIP-seq Analysis

Rendered fromintegrative_analysis.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-05-03
Started: 2020-05-04

Denovo Motif Discovery Using DREME

Rendered fromcore_dreme.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-05-03
Started: 2020-05-12

Install MEME

Rendered frominstall_guide.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-12-03
Started: 2020-05-13

Motif Comparison using TomTom

Rendered fromcore_tomtom.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-05-03
Started: 2020-05-12

Motif Enrichment Testing using AME

Rendered fromcore_ame.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-04-04
Started: 2020-05-12

Motif Scanning using FIMO

Rendered fromcore_fimo.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-05-03
Started: 2020-05-12

Tidying Motif Metadata

Rendered fromtidy_motifs.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2021-03-31
Started: 2020-05-08

Readme and manuals

Help Manual

Help pageTopics
Add nucleic acid sequence of regions to metadata columnadd_sequence
Compare AME heatmap methodsame_compare_heatmap_methods
Check user's MEME installcheck_meme_install
Drop best match columns from tomtom resultsdrop_best_match
Example runAme() outputexample_ame
runAme() output for example_chip_summits split by binding descriptionexample_ame_large
Annotated Transcription Factor ChIP-seq summitsexample_chip_summits
Example runDreme() outputexample_dreme
runDreme() output for example_chip_summits split by binding descriptionexample_dreme_by_binding
Example runDreme() output after passing to runTomTom()example_dreme_tomtom
Example runFimo() outputexample_fimo
Example ChIP-seq peaksexample_peaks
RNAseq data from Early and Late Drosophila wingsexample_rnaseq
Example runTomTom() outputexample_tomtom
Force best tomtom match by idforce_best_match
Get sequence from GRangesget_sequence
Check for duplicated motif matriceshas_duplicate_motifs
Parse AME outputimportAme
Import Dreme output from previous runimportDremeXML
Import FIMO resultsimportFimo
Import MEME resultsimportMeme
Import Streme output from previous runimportStremeXML
Import tomtom data from previous runimportTomTomXML
Returns logical vector indicating valid MEME-Suite install statusmeme_is_installed
Nest TomTom results columns into a data.frame column named "tomtom"nest_tomtom
Plot AME heatmap clustered by similarity in detected motifsplot_ame_heatmap
Visualize a heatmap of aligned sequencesplot_sequence_heatmap
Remove duplicated motif entriesremove_duplicate_motifs
Motif enrichment using AMErunAme runAme.BStringSetList runAme.default runAme.list
Denovo motif discovery of target regions using DREMErunDreme
Find instances of motifs using FIMOrunFimo
Identify motifs with MEMErunMeme runMeme.BStringSetList runMeme.default runMeme.list
Denovo motif discovery of target regions using STREMErunStreme
Run TomTom on target motifsrunTomTom
Update best match info by ranking of tomtom dataupdate_best_match
Compare top tomtom hits to original motifview_tomtom_hits
Write fasta file from stringsetwrite_fasta