See package website for full vignette | Introduction | Installing the MEME Suite | Detecting the MEME Suite | FAQS | Session Info
Package: memes 1.21.0
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:
memes_1.21.0.tar.gz
memes_1.21.0.zip(r-4.7)memes_1.21.0.zip(r-4.6)memes_1.21.0.zip(r-4.5)
memes_1.21.0.tgz(r-4.6-any)memes_1.21.0.tgz(r-4.5-any)
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memes_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
memes/json (API)
| # Install 'memes' in R: |
| install.packages('memes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/snystrom/memes/issues
Datasets:
- example_ame - Example runAme() output
- example_ame_large - RunAme() output for example_chip_summits split by binding description
- example_chip_summits - Annotated Transcription Factor ChIP-seq summits
- example_dreme - Example runDreme() output
- example_dreme_by_binding - RunDreme() output for example_chip_summits split by binding description
- example_dreme_tomtom - Example runDreme
- example_fimo - Example runFimo() output
- example_peaks - Example ChIP-seq peaks
- example_rnaseq - RNAseq data from Early and Late Drosophila wings
- example_tomtom - Example runTomTom() output
On BioConductor:memes-1.21.0(bioc 3.24)memes-1.20.0(bioc 3.23)
dataimportfunctionalgenomicsgeneregulationmotifannotationmotifdiscoverysequencematchingsoftware
Last updated from:212302350c. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 257 | ||
| linux-devel-x86_64 | WARNING | 358 | ||
| source / vignettes | OK | 333 | ||
| linux-release-x86_64 | WARNING | 279 | ||
| macos-release-arm64 | WARNING | 145 | ||
| macos-oldrel-arm64 | WARNING | 129 | ||
| windows-devel | WARNING | 263 | ||
| windows-release | WARNING | 277 | ||
| windows-oldrel | WARNING | 252 | ||
| wasm-release | OK | 206 |
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:askpassBiocGenericsBiostringsbitbit64briocallrclicliprcmdfuncpp11crayoncredentialscurldescdiffobjdplyrevaluatefarverfsgenericsGenomicRangesgertggplot2gitcredsgluegtablehmshttr2iniIRangesisobandjsonlitelabelinglifecyclemagrittrMASSMatrixGenericsmatrixStatsopensslotelpatchworkpillarpkgbuildpkgconfigpkgloadpraiseprettyunitsprocessxprogresspspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppThreadreadrrlangrprojrootrstudioapiS4VectorsS7scalesSeqinfostringistringrsystestthattibbletidyrtidyselecttzdbuniversalmotifusethisutf8vctrsviridisLitevroomwaldowhiskerwithrxml2XVectoryamlzip
Install MEME
Last update: 2021-12-03
Started: 2020-05-13
ChIP-seq Analysis
See package website for full vignette | Introduction | Prepare peaks for analysis | Determinants of ectopic and orphan binding | Pre-filtering database for expressed transcription factors | Examination of binding categories with AME | Visualizing AME results | Reducing redundant motif hits | AME Heatmap Visualization | De-novo motif similarity by binding | Test de-novo motif enrichment using AME | Motifs in opening vs closing sites | Scanning for motif matches using FIMO | Counting the number of motifs per peak | Centrality of E93 motif | Conclusion | References | Session Info
Last update: 2021-05-03
Started: 2020-05-04
Denovo Motif Discovery Using DREME
See package website for full vignette | Aliased flags | Updating motif information | Notes about shuffled control sequences | Analysis on Multiple Groups and Differential Analysis | Discriminative analysis using list input | Importing previous data | Saving data from DREME Web Server | Citation | Licensing Restrictions | Session Info
Last update: 2021-05-03
Started: 2020-05-12
Motif Comparison using TomTom
See package website for full vignette | Introduction | Accepted database formats | Setting a default database | Input types | Output data | Manipulating the assigned best match | Visualize data | Importing previous data | Saving data from TomTom Web Server | Citation | Licensing Restrictions | Session Info
Last update: 2021-05-03
Started: 2020-05-12
Motif Scanning using FIMO
See package website for full vignette | Inputs | Sequence Inputs: | Motif Inputs: | Note about default settings | Data integration with join operations | Identifying matched sequence | Importing Data from previous FIMO Runs | Saving data from FIMO Web Server | Citation | Licensing Restrictions | Session Info
Last update: 2021-05-03
Started: 2020-05-12
Motif Enrichment Testing using AME
Sequence Input | Database Input | Setting a default database | Running AME | Running AME on multiple groups | Discriminative analysis using list input | Output Format | Visualizing Results as Heatmap | Complex Heatmap Example | Issues with Heatmap Visualization | Importing Previous Data | Saving data from AME Web Server | Citation | Licensing Restrictions | Session Info
Last update: 2021-04-04
Started: 2020-05-12
Tidying Motif Metadata
A few reality checks | Removing duplicate motif matrices | Session Info
Last update: 2021-03-31
Started: 2020-05-08
