├── .gitignore ├── DESCRIPTION ├── Data ├── genes.bed ├── sQTLs-FDR10-CEU.tsv.gz ├── sQTLs-FDR10-FIN.tsv.gz ├── sQTLs-FDR10-GBR.tsv.gz ├── sQTLs-FDR10-TSI.tsv.gz ├── sQTLs-FDR10-YRI.tsv.gz ├── snps-012coded.tsv └── transExpression.tsv.gz ├── NAMESPACE ├── R ├── adonis.comp.R ├── classify.events.R ├── compFscore.R ├── compPvalue.R ├── compute.null.R ├── hellingerDist.R ├── index.genotype.R ├── md.trans.R ├── nbDiffPt.R ├── permutest.betadisper.R ├── prepare.trans.exp.R ├── read.bedix.R ├── relativize.R ├── sqtl.seeker.R ├── sqtls.R └── te.dispersion.R ├── README.md ├── TODO.md ├── docs ├── README.md ├── SplicingEventClassification.Rmd ├── SplicingEventClassification.md ├── SplicingEventClassification_files │ └── figure-markdown_github │ │ ├── unnamed-chunk-11-1.png │ │ ├── unnamed-chunk-7-1.png │ │ └── unnamed-chunk-8-1.png └── splicingEventsClassification.png ├── install.R ├── installOnR.3.1.R ├── man ├── adonis.comp.Rd ├── classify.events.Rd ├── compFscore.Rd ├── compPvalue.Rd ├── compute.null.Rd ├── hellingerDist.Rd ├── index.genotype.Rd ├── md.trans.Rd ├── nbDiffPt.Rd ├── permutest.betadisper.Rd ├── prepare.trans.exp.Rd ├── read.bedix.Rd ├── relativize.Rd ├── sQTLseekeR-package.Rd ├── sqtl.seeker.Rd ├── sqtls.Rd └── te.dispersion.Rd ├── scripts ├── .BatchJobs.R ├── benchmark-sQTLseekeR.R ├── cluster.tmpl ├── makeClusterFunctionsAdaptive.R ├── run-example-BatchJobs-manySNPs.R ├── run-example-BatchJobs.R ├── run-example-preproc.sh └── run-example.R └── tests ├── testthat.R └── testthat ├── test-Fcomp.R ├── test-PVcomp.R ├── test-indexGeno.R ├── test-prepareTE.R └── test-sqtlseeker.R /.gitignore: -------------------------------------------------------------------------------- 1 | *~ -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /Data/genes.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/genes.bed -------------------------------------------------------------------------------- /Data/sQTLs-FDR10-CEU.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/sQTLs-FDR10-CEU.tsv.gz -------------------------------------------------------------------------------- /Data/sQTLs-FDR10-FIN.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/sQTLs-FDR10-FIN.tsv.gz -------------------------------------------------------------------------------- /Data/sQTLs-FDR10-GBR.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/sQTLs-FDR10-GBR.tsv.gz -------------------------------------------------------------------------------- /Data/sQTLs-FDR10-TSI.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/sQTLs-FDR10-TSI.tsv.gz -------------------------------------------------------------------------------- /Data/sQTLs-FDR10-YRI.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/sQTLs-FDR10-YRI.tsv.gz -------------------------------------------------------------------------------- /Data/snps-012coded.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/snps-012coded.tsv -------------------------------------------------------------------------------- /Data/transExpression.tsv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/Data/transExpression.tsv.gz -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/adonis.comp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/adonis.comp.R -------------------------------------------------------------------------------- /R/classify.events.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/classify.events.R -------------------------------------------------------------------------------- /R/compFscore.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/compFscore.R -------------------------------------------------------------------------------- /R/compPvalue.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/compPvalue.R -------------------------------------------------------------------------------- /R/compute.null.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/compute.null.R -------------------------------------------------------------------------------- /R/hellingerDist.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/hellingerDist.R -------------------------------------------------------------------------------- /R/index.genotype.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/index.genotype.R -------------------------------------------------------------------------------- /R/md.trans.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/md.trans.R -------------------------------------------------------------------------------- /R/nbDiffPt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/nbDiffPt.R -------------------------------------------------------------------------------- /R/permutest.betadisper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/permutest.betadisper.R -------------------------------------------------------------------------------- /R/prepare.trans.exp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/prepare.trans.exp.R -------------------------------------------------------------------------------- /R/read.bedix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/read.bedix.R -------------------------------------------------------------------------------- /R/relativize.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/relativize.R -------------------------------------------------------------------------------- /R/sqtl.seeker.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/sqtl.seeker.R -------------------------------------------------------------------------------- /R/sqtls.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/sqtls.R -------------------------------------------------------------------------------- /R/te.dispersion.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/R/te.dispersion.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/README.md -------------------------------------------------------------------------------- /TODO.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/TODO.md -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/SplicingEventClassification.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/SplicingEventClassification.Rmd -------------------------------------------------------------------------------- /docs/SplicingEventClassification.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/SplicingEventClassification.md -------------------------------------------------------------------------------- /docs/SplicingEventClassification_files/figure-markdown_github/unnamed-chunk-11-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/SplicingEventClassification_files/figure-markdown_github/unnamed-chunk-11-1.png -------------------------------------------------------------------------------- /docs/SplicingEventClassification_files/figure-markdown_github/unnamed-chunk-7-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/SplicingEventClassification_files/figure-markdown_github/unnamed-chunk-7-1.png -------------------------------------------------------------------------------- /docs/SplicingEventClassification_files/figure-markdown_github/unnamed-chunk-8-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/SplicingEventClassification_files/figure-markdown_github/unnamed-chunk-8-1.png -------------------------------------------------------------------------------- /docs/splicingEventsClassification.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/docs/splicingEventsClassification.png -------------------------------------------------------------------------------- /install.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/install.R -------------------------------------------------------------------------------- /installOnR.3.1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/installOnR.3.1.R -------------------------------------------------------------------------------- /man/adonis.comp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/adonis.comp.Rd -------------------------------------------------------------------------------- /man/classify.events.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/classify.events.Rd -------------------------------------------------------------------------------- /man/compFscore.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/compFscore.Rd -------------------------------------------------------------------------------- /man/compPvalue.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/compPvalue.Rd -------------------------------------------------------------------------------- /man/compute.null.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/compute.null.Rd -------------------------------------------------------------------------------- /man/hellingerDist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/hellingerDist.Rd -------------------------------------------------------------------------------- /man/index.genotype.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/index.genotype.Rd -------------------------------------------------------------------------------- /man/md.trans.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/md.trans.Rd -------------------------------------------------------------------------------- /man/nbDiffPt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/nbDiffPt.Rd -------------------------------------------------------------------------------- /man/permutest.betadisper.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/permutest.betadisper.Rd -------------------------------------------------------------------------------- /man/prepare.trans.exp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/prepare.trans.exp.Rd -------------------------------------------------------------------------------- /man/read.bedix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/read.bedix.Rd -------------------------------------------------------------------------------- /man/relativize.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/relativize.Rd -------------------------------------------------------------------------------- /man/sQTLseekeR-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/sQTLseekeR-package.Rd -------------------------------------------------------------------------------- /man/sqtl.seeker.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/sqtl.seeker.Rd -------------------------------------------------------------------------------- /man/sqtls.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/sqtls.Rd -------------------------------------------------------------------------------- /man/te.dispersion.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/man/te.dispersion.Rd -------------------------------------------------------------------------------- /scripts/.BatchJobs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/.BatchJobs.R -------------------------------------------------------------------------------- /scripts/benchmark-sQTLseekeR.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/benchmark-sQTLseekeR.R -------------------------------------------------------------------------------- /scripts/cluster.tmpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/cluster.tmpl -------------------------------------------------------------------------------- /scripts/makeClusterFunctionsAdaptive.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/makeClusterFunctionsAdaptive.R -------------------------------------------------------------------------------- /scripts/run-example-BatchJobs-manySNPs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/run-example-BatchJobs-manySNPs.R -------------------------------------------------------------------------------- /scripts/run-example-BatchJobs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/run-example-BatchJobs.R -------------------------------------------------------------------------------- /scripts/run-example-preproc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/run-example-preproc.sh -------------------------------------------------------------------------------- /scripts/run-example.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/scripts/run-example.R -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/test-Fcomp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/tests/testthat/test-Fcomp.R -------------------------------------------------------------------------------- /tests/testthat/test-PVcomp.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/tests/testthat/test-PVcomp.R -------------------------------------------------------------------------------- /tests/testthat/test-indexGeno.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/tests/testthat/test-indexGeno.R -------------------------------------------------------------------------------- /tests/testthat/test-prepareTE.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/tests/testthat/test-prepareTE.R -------------------------------------------------------------------------------- /tests/testthat/test-sqtlseeker.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jmonlong/sQTLseekeR/HEAD/tests/testthat/test-sqtlseeker.R --------------------------------------------------------------------------------