metagene: A package to produce metagene plots

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metagene")
AuthorCharles 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>.
Bioconductor views Alignment ChIPSeq Coverage Genetics MultipleComparison Sequencing
Date of publicationNone
MaintainerCharles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>
LicenseArtistic-2.0 | file LICENSE
Version2.8.0

View on Bioconductor

Files

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

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