ASpli: Analysis of alternative splicing using RNA-Seq

Integrative pipeline for the analyisis of alternative splicing using RNAseq.

Author
Estefania Mancini, Marcelo Yanovsky and Ariel Chernomoretz
Date of publication
None
Maintainer
Estefania Mancini <emancini@leloir.org.ar>
License
GPL
Version
1.0.0

View on Bioconductor

Man pages

acc_AS
Accessors for ASpliAS object
acc_counts
Accessors for ASpliCounts object
acc_DU
Accessors for ASpliDU object
acc_features
Accessors for ASpliFeatures object
AsDiscover-methods
Report PSI and PIR using experimental junctions
ASpliAS-class
Class '"ASpliAS"'
ASpliCounts
Class '"ASpliCounts"'
ASpliCounts-class
Class '"ASpliCounts"'
ASpliDU-class
Class '"ASpliDU"'
ASpliFeatures-class
Class '"ASpliFeatures"'
ASpli-package
Analysis of alternative splicing using RNAseq
binGenome
Feature coordinates extraction
binGenome-methods
Feature coordinates extraction
DUreport
Differential gene expression and differential bin/junction...
DUreport_DEXSeq
Differential gene expression and differential bin/junction...
loadBAM
Load BAM files
plotTopTags
Coverage plots
rds
Divides read counts by gene and bin length
readCounts
Summarize read overlaps
show-methods
Display a summary of data contained in ASpliObjects
write
Write results
write-methods
Write results

Files in this package

ASpli/DESCRIPTION
ASpli/NAMESPACE
ASpli/NEWS
ASpli/R
ASpli/R/ASDiscover_functions.R
ASpli/R/ASpli_methods.R
ASpli/R/ASpli_show_methods.R
ASpli/R/DUreport_functions.R
ASpli/R/binGenome_functions.R
ASpli/R/bins_DEXSeq.R
ASpli/R/loadBam_function.R
ASpli/R/plotTopTags_function.R
ASpli/R/readCounts_functions.R
ASpli/build
ASpli/build/vignette.rds
ASpli/inst
ASpli/inst/NEWS
ASpli/inst/doc
ASpli/inst/doc/ASpli.R
ASpli/inst/doc/ASpli.Rnw
ASpli/inst/doc/ASpli.pdf
ASpli/inst/extdata
ASpli/inst/extdata/chr14.sqlite
ASpli/man
ASpli/man/ASpli-package.Rd
ASpli/man/ASpliAS-class.Rd
ASpli/man/ASpliCounts-class.Rd
ASpli/man/ASpliCounts.Rd
ASpli/man/ASpliDU-class.Rd
ASpli/man/ASpliFeatures-class.Rd
ASpli/man/AsDiscover-methods.Rd
ASpli/man/DUreport.Rd
ASpli/man/DUreport_DEXSeq.Rd
ASpli/man/acc_AS.Rd
ASpli/man/acc_DU.Rd
ASpli/man/acc_counts.Rd
ASpli/man/acc_features.Rd
ASpli/man/binGenome-methods.Rd
ASpli/man/binGenome.Rd
ASpli/man/loadBAM.Rd
ASpli/man/plotTopTags.Rd
ASpli/man/rds.Rd
ASpli/man/readCounts.Rd
ASpli/man/show-methods.Rd
ASpli/man/write-methods.Rd
ASpli/man/write.Rd
ASpli/vignettes
ASpli/vignettes/ASpli.Rnw
ASpli/vignettes/ASpli.bib
ASpli/vignettes/LRR1_E005.png
ASpli/vignettes/binDefinition.png
ASpli/vignettes/pir.png
ASpli/vignettes/psi_altSS.png
ASpli/vignettes/psi_es.png
ASpli/vignettes/venn.png
ASpli/vignettes/wf.png