metagene: A package to produce metagene plots

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This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.

Author
Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>, Fabien Claude Lamaze <fabien.lamaze.1@ulaval.ca>, Rawane Samb <rawane.samb.1@ulaval.ca>, Astrid Louise Deschenes <Astrid-Louise.Deschenes@crchudequebec.ulaval.ca> and Arnaud Droit <arnaud.droit@crchuq.ulaval.ca>.
Date of publication
None
Maintainer
Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>
License
Artistic-2.0 | file LICENSE
Version
2.6.1

View on Bioconductor

Man pages

Bam_Handler
A class to manage BAM files.
get_demo_bam_files
Get BAM filenames for demo
get_demo_design
Get a demo design object
get_demo_metagene
Get a demo metagene object
get_demo_regions
Get regions filenames for demo
get_promoters_txdb
Extract Entrez genes promoters from TxDb object.
metagene
A class to manage metagene analysis.
permutation_test
Perform a permutation test on 2 matrices
plot_metagene
Produce a metagene plot
promoters_hg18
Promoters regions of hg18 Entrez genes.
promoters_hg19
Promoters regions of hg19 Entrez genes.
promoters_mm10
Promoters regions of mm10 Entrez genes.
promoters_mm9
Promoters regions of mm9 Entrez genes.

Files in this package

metagene/DESCRIPTION
metagene/LICENSE
metagene/NAMESPACE
metagene/NEWS
metagene/R
metagene/R/Utilities.R
metagene/R/bam_handler.R
metagene/R/data.R
metagene/R/demo.R
metagene/R/metagene.R
metagene/R/normalization.R
metagene/R/parallel_job.R
metagene/R/permutation.R
metagene/R/plot_metagene.R
metagene/R/stats.R
metagene/R/sysdata.rda
metagene/README.md
metagene/build
metagene/build/vignette.rds
metagene/data
metagene/data/promoters_hg18.RData
metagene/data/promoters_hg19.RData
metagene/data/promoters_mm10.RData
metagene/data/promoters_mm9.RData
metagene/inst
metagene/inst/doc
metagene/inst/doc/metagene.R
metagene/inst/doc/metagene.Rmd
metagene/inst/doc/metagene.html
metagene/inst/extdata
metagene/inst/extdata/align1.rep1.bam
metagene/inst/extdata/align1.rep1.bam.bai
metagene/inst/extdata/align1_rep1.bam
metagene/inst/extdata/align1_rep1.bam.bai
metagene/inst/extdata/align1_rep1.bed
metagene/inst/extdata/align1_rep2.bam
metagene/inst/extdata/align1_rep2.bam.bai
metagene/inst/extdata/align2_rep1.bam
metagene/inst/extdata/align2_rep1.bam.bai
metagene/inst/extdata/align2_rep2.bam
metagene/inst/extdata/align2_rep2.bam.bai
metagene/inst/extdata/coverage.bam
metagene/inst/extdata/coverage.bam.bai
metagene/inst/extdata/ctrl.bam
metagene/inst/extdata/ctrl.bam.bai
metagene/inst/extdata/ctrl.bed
metagene/inst/extdata/design.txt
metagene/inst/extdata/different_header.bam
metagene/inst/extdata/different_header.bam.bai
metagene/inst/extdata/list1.bed
metagene/inst/extdata/list1.broadPeak
metagene/inst/extdata/list1.narrowPeak
metagene/inst/extdata/list1.txt
metagene/inst/extdata/list2.bed
metagene/inst/extdata/list2.txt
metagene/inst/extdata/list_coverage.bed
metagene/inst/extdata/lists.bed
metagene/inst/extdata/not_indexed.bam
metagene/inst/unitTests
metagene/inst/unitTests/Makefile
metagene/inst/unitTests/test_bam_handler.R
metagene/inst/unitTests/test_demo.R
metagene/inst/unitTests/test_metagene.R
metagene/inst/unitTests/test_parallel_job.R
metagene/inst/unitTests/test_permutation.R
metagene/inst/unitTests/test_stats.R
metagene/inst/unitTests/test_utilities.R
metagene/man
metagene/man/Bam_Handler.Rd
metagene/man/get_demo_bam_files.Rd
metagene/man/get_demo_design.Rd
metagene/man/get_demo_metagene.Rd
metagene/man/get_demo_regions.Rd
metagene/man/get_promoters_txdb.Rd
metagene/man/metagene.Rd
metagene/man/permutation_test.Rd
metagene/man/plot_metagene.Rd
metagene/man/promoters_hg18.Rd
metagene/man/promoters_hg19.Rd
metagene/man/promoters_mm10.Rd
metagene/man/promoters_mm9.Rd
metagene/tests
metagene/tests/runTests.R
metagene/vignettes
metagene/vignettes/metagene.Rmd