ASpli-package: Analysis of Alternative Splicing Using RNAseq
In chernolab/ASpli: Analysis of Alternative Splicing Using RNA-Seq

Description Details Author(s) References Examples

ASpli is an integrative and flexible package that facilitates the characterization of genome-wide changes in AS under different experimental conditions. ASpli analyzes the differential usage of introns, exons, and splice junctions using read counts, and estimates the magnitude of changes in AS by calculating differences in the percentage of exon inclusion or intron retention using splice junctions. This integrative approach allows the identification of changes in both annotated and novel AS events.

ASpli allows users to produce self-explanatory intermediate outputs, based on the aim of their analysis. A typical workflow involves parsing the genome annotation into new features called bins, overlapping read alignments against those bins, and inferring differential bin usage based on the number of reads aligning to the bins and junctions.

Package:	ASpli
Type:	Package
Version:	1.5.1
Date:	2018-02-22
License:	GPL
Depends:	methods, GenomicRanges, GenomicFeatures, edgeR, methods, BiocGenerics, IRanges, GenomicAlignments, Gviz

Estefania Mancini, Andres Rabinovich, Javier Iserte, Marcelo Yanovsky, Ariel Chernomoretz

Acute effects of light on alternative splicing in light-grown plants. Photochemistry and Photobiology. Mancini, E, Sanchez, S, Romanowsky, A, Yanovsky, MJ. DOI: 10.1111/php.12550
GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms in Arabidopsis thaliana. Proceedings of the National Academy of Sciences. Schlaen, RG, Mancini, E, Sanchez, SE, Perez-Santangelo, S, Rugnone, ML, Simpson, CG, Brown, JWS, Zhang, X, Chernomoretz, A, Yanovsky, MJ. DOI:10.1073/pnas.1504541112
Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome. BMC Genomics. Hernando, E, Sanchez, S, Mancini, E, Yanovsky MJ. DOI:10.1186/s12864-015-1399-2
A role for LSM genes in the regulation of circadian rhythms. Proceedings of the National Academy of Sciences. Perez Santangelo, S, Mancini, E, Francey, LJ, Schlaen, RG, Chernomoretz, A, Hogenesch, JB, Yanovsky MJ. DOI: 10.1073/pnas.1409791111
The dengue virus NS5 protein intrudes in the cellular spliceosome and modulates splicing. PLOS Pathogens. De Maio, F., Risso, G., Iglesias, G., Shah, P, Pozzi, B., Gebhard, L., Mammi, L., Mancini, E., Yanovsky, M., Andino, R., Krogan, N., Srebrow, A. and Gamarnik, A. DOI:10.1371/journal.ppat.1005841

 
library(GenomicFeatures)
gtfFileName <- aspliExampleGTF()
genomeTxDb <- makeTxDbFromGFF( gtfFileName )
features <- binGenome( genomeTxDb )
BAMFiles <- aspliExampleBamList()
targets <- data.frame( 
  row.names = paste0('Sample',c(1:12)),
  bam = BAMFiles,
  f1 = c( 'A','A','A','A','A','A',
          'B','B','B','B','B','B'),
  f2 = c( 'C','C','C','D','D','D',
          'C','C','C','D','D','D'),
  stringsAsFactors = FALSE)
  getConditions(targets)
  mBAMs <- data.frame(bam      = sub("_[02]","",targets$bam[c(1,4,7,10)]),
                      condition= c("A_C","A_D","B_C","B_D"))

gbcounts  <- gbCounts( features = features, 
                           targets = targets, 
                           minReadLength = 100, maxISize = 50000,
                           libType="SE", 
                           strandMode=0)
asd   <- jCounts(counts = gbcounts, 
                     features = features, 
                     minReadLength = 100,
                     libType="SE", 
                     strandMode=0)
                     
   
gb      <- gbDUreport(counts=gbcounts,
contrast = c( 1, -1, -1, 1 ) )
jdur    <- jDUreport(asd, 
                     contrast =  c( 1, -1, -1, 1 ) ,
                     mergedBams = mBAMs)
sr      <- splicingReport(gb, jdur, counts =gbcounts    )
is      <- integrateSignals(sr,asd)