Files in kendomaniac/docker4seq
Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

.Rbuildignore
.gitignore
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
R/annotatingByGtf.R R/bwa.R R/bwaIndexUcsc.R R/casc.allZeros.R R/casc.checkCountDepth.R R/casc.impute.R R/casc.scnorm.R R/cascKoptimization.R R/cascOutputReformat.R R/cascStep1.R R/cascStep2.R R/cascStep4.R R/cascTable.R R/chipseq.R R/chipseqCounts.R R/demultiplexing.R R/downloadContainers.R R/experimentPower.R R/fastqc.R R/filterCounts.R R/gatkDna.R R/indropCounts.R R/lorenzFilter.R R/mirnaCounts.R R/mirnaCovar.R R/oncosnpAnnotation.R R/pca.R R/rnaseqCounts.R R/rsemAnnotate.R R/rsemBw.R R/rsemStar.R R/rsemstarIndex.R R/rsemstarUcscIndex.R R/runDocker.R R/salmonAnnotation.R R/salmonCounts.R R/salmonIndex.R R/sampleSize.R R/samples2experiment.R R/skewer.R R/star2steps.R R/starChimeric.R R/testDocker.R R/testSeqBox.R R/wrapperDeseq2.R R/wrapperPdx.R R/wrapperSalmon.R R/xenome.R R/xenomeIndex.R README.md
docker4seq.Rproj
inst/containers/containers.txt
inst/examples/4t1_counts.txt
inst/examples/SampleSheet.csv
inst/examples/mb231_counts.txt
inst/examples/readme.txt
inst/extras/indrop.yaml
inst/img/buettner_fig19c.jpeg
inst/img/buettner_fig19e.jpeg
inst/img/casc_description1.jpeg
inst/img/casc_description2.jpeg
inst/img/casc_description3.jpeg
inst/img/chipseq0.jpeg
inst/img/chipseq1.jpeg
inst/img/chipseq3.jpeg
inst/img/chipseq_performance.jpg
inst/img/chipseq_performance_bis.jpg
inst/img/containers.jpeg
inst/img/counts1.jpeg
inst/img/counts2.jpeg
inst/img/counts3.jpeg
inst/img/de1.jpeg
inst/img/de2.jpeg
inst/img/de3.jpeg
inst/img/es.jpeg
inst/img/expp1.jpeg
inst/img/jaccard.jpeg
inst/img/lorenz1.jpeg
inst/img/lorenz2.jpeg
inst/img/lorenz3.jpeg
inst/img/mirna1.jpeg
inst/img/mirna2.jpeg
inst/img/mirna3.jpeg
inst/img/mirna_covars.jpeg
inst/img/mirna_performace.jpg
inst/img/mirnaseq_performance_bis.jpg
inst/img/mrna_performace.jpg
inst/img/mrna_performance.jpg
inst/img/mrna_performance_bis.jpg
inst/img/pca1.jpeg
inst/img/pca2.jpeg
inst/img/rnaseq1.jpeg
inst/img/rnaseq2.jpeg
inst/img/rnaseq3.jpeg
inst/img/rnaseq4.jpeg
inst/img/rnaseq5.jpeg
inst/img/rnaseq6.jpeg
inst/img/rnaseq7.jpeg
inst/img/salmonCounts.jpeg
inst/img/salmonIndex.jpeg
inst/img/salmon_rsem.jpg
inst/img/samplesize1.jpeg
inst/img/scimpute.jpeg
inst/img/scnorm.jpeg
inst/img/silhouette.jpeg
inst/img/silhouette.stability.jpg
inst/img/silhouette1.jpeg
inst/img/simlr.jpeg
inst/img/simlr1.jpeg
inst/img/ss.jpeg
inst/img/summary_table.jpeg
man/bwa.Rd man/bwaIndexUcsc.Rd man/cascImpute.Rd man/cascKoptimization.Rd man/cascOutputReformat.Rd man/cascSelFeatures.Rd man/cascStep1.Rd man/cascStep2.Rd man/checkCountDepth.Rd man/chipseq.Rd man/chipseqCounts.Rd man/counts2log.Rd man/demultiplexing.Rd man/dockerTest.Rd man/downloadContainers.Rd man/experimentPower.Rd man/fastqc.Rd man/filterCounts.Rd man/filterZeros.Rd man/gatkDNA.Rd man/indropCounts.Rd man/lorenzFilter.Rd man/mirnaCounts.Rd man/mirnaCovar.Rd man/oncosnpAnnotation.Rd man/pca.Rd man/rnaseqCounts.Rd man/rsemBw.Rd man/rsemanno.Rd man/rsemannoByGtf.Rd man/rsemstar.Rd man/rsemstarIndex.Rd man/rsemstarUscsIndex.Rd man/runDocker.Rd man/salmonAnnotation.Rd man/salmonCounts.Rd man/salmonIndex.Rd man/sample2experiment.Rd man/sampleSize.Rd man/scnorm.Rd man/skewer.Rd man/star2steps.Rd man/starChimeric.Rd man/testSeqbox.Rd man/wrapperDeseq2.Rd man/wrapperPdx.Rd man/wrapperSalmon.Rd man/xenome.Rd man/xenomeIndex.Rd
supplementary_data.html
supplementary_data.md vignettes/casc.Rmd vignettes/docker4seq.Rmd
vignettes/rsconnect/documents/casc.Rmd/rpubs.com/rpubs/Document.dcf
vignettes/rsconnect/documents/casc.Rmd/rpubs.com/rpubs/Publish Document.dcf
vignettes/rsconnect/documents/docker4seq.Rmd/rpubs.com/rpubs/Document.dcf
vignettes/rsconnect/documents/docker4seq.Rmd/rpubs.com/rpubs/Publish Document.dcf
vignettes/rsconnect/documents/supplementary_data.Rmd/rpubs.com/rpubs/Document.dcf
vignettes/skeleton.Rmd vignettes/supplementary_data.Rmd
kendomaniac/docker4seq documentation built on Jan. 14, 2018, 3:33 p.m.