Introduction | Creating a metagene object | Specifying alignment files (BAM files) | Specifying genomic regions | Defining regions using BED, narrowPeak, broadPeak and GTF files | Defining contiguous regions using GRanges or GRangesList objects | GRangesList objects for stitching ranges together | Generating common ranges (Promoters, gene bodies) | Grouping regions and bam files | Grouping bam files | Using an experimental design | Using design metadata | Grouping regions | Grouping regions using a GRangesList | Grouping regions using metadata | Intermediary processing steps and further parameters | Arguments, results caching and chaining | metagene2$new | group_coverages | bin_coverages | split_coverages_by_regions | calculate_ci | add_metadata | plot | Manipulating the metagene2 objects | Getters | get_params | get_bam_count | get_regions | get_raw_coverages | get_normalized_coverages | clone | Managing large datasets | Plotting heatmaps | Differences with metagene | Better-defined operations | Better parameter management | Working with metadata | True RNA-seq metagenes | Miscellaneous changes and improvements
Package: metagene2 1.29.0
Eric Fournier
metagene2: A package to produce metagene plots
This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.
Authors:
metagene2_1.29.0.tar.gz
metagene2_1.29.0.zip(r-4.7)metagene2_1.29.0.zip(r-4.6)metagene2_1.29.0.zip(r-4.5)
metagene2_1.29.0.tgz(r-4.6-any)metagene2_1.29.0.tgz(r-4.5-any)
metagene2_1.29.0.tar.gz(r-4.7-any)metagene2_1.29.0.tar.gz(r-4.6-any)
metagene2_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metagene2/json (API)
| # Install 'metagene2' in R: |
| install.packages('metagene2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/arnauddroitlab/metagene2/issues
On BioConductor:metagene2-1.29.0(bioc 3.24)metagene2-1.28.0(bioc 3.23)
chipseqgeneticsmultiplecomparisoncoveragealignmentsequencing
Last updated from:433a7093e2. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 256 | ||
| linux-devel-x86_64 | WARNING | 496 | ||
| source / vignettes | OK | 301 | ||
| linux-release-x86_64 | WARNING | 451 | ||
| macos-release-arm64 | WARNING | 242 | ||
| macos-oldrel-arm64 | WARNING | 193 | ||
| windows-devel | WARNING | 355 | ||
| windows-release | WARNING | 415 | ||
| windows-oldrel | WARNING | 341 | ||
| wasm-release | OK | 185 |
Exports:as_is_region_orderBam_Handlercoverage_orderget_demo_bam_filesget_demo_designget_demo_metageneget_demo_region_filenamesget_demo_regionsget_demo_rna_bam_filesget_demo_rna_regionsmetagene2metagene2_heatmapplot_metagene
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurldata.tableDelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrpurrrR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Returns an "as-is" ordering of regions. | as_is_region_order |
| A class to manage BAM files. | Bam_Handler |
| Determines ordering of regions as a function of coverage. | coverage_order |
| Get BAM filenames for demo | get_demo_bam_files |
| Get a demo design object | get_demo_design |
| Get a demo metagene object | get_demo_metagene |
| Get regions filenames for demo | get_demo_region_filenames |
| Get demo regions | get_demo_regions |
| Get BAM filenames for demo | get_demo_rna_bam_files |
| Get demo regions | get_demo_rna_regions |
| A class to manage metagene analysis. | metagene2 |
| Plots a heatmap of coverages from a metagene2 object. | metagene2_heatmap |
| Produce a metagene plot | plot_metagene |
