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

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/.gitignore

R/annotatingByGtf.R R/annotatingByGtfchipseq.R R/anovaLike.R R/bowtie2.R R/bowtie2Index.R R/bwa.R R/bwaIndex.R R/bwaIndexUcsc.R R/cdhit.R R/chipseq.R R/chipseqCounts.R R/circexplorer2.R R/circrnaAnnotations.R R/circrnaBSJunctions.R R/circrnaClassification.R R/circrnaMergePredictions.R R/circrnaOverlapResults.R R/circrnaPrepareFiles.R R/circrnaQuantification.R R/circrnaReformat.R R/ciri2.R R/ciri_as.R R/cutadapt.R R/deeptoolBwig.R R/demultiplexing.R R/downloadContainers.R R/downloadGeneInfo.R R/expandsReformat.R R/experimentPower.R R/fasterq.dump.R R/fastq2fasta.R R/fastqc.R R/filterCounts.R R/gatkDna.R R/hashclone.R R/heatmapBase.R R/heatmaply.R R/kraken.R R/macs2.R R/mergeData.R R/mirnaCounts.R R/mirnaCovar.R R/multiQC.R R/oncosnpAnnotation.R R/oncosnpIllumina.R R/pca.R R/platypus.R R/platypusFilter.R R/pubmedNet.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/skeleton.R R/skewer.R R/skewerXSergio.R R/sncRNA.R R/snvPreprocessing.R R/star.R R/star2steps.R R/starChimeric.R R/starChipIndex.R R/starchipCircle.R R/testDocker.R R/testSeqBox.R R/trimFasta.R R/wrapperCiri.R R/wrapperDeseq2.R R/wrapperPdx.R R/wrapperSTARChip.R R/wrapperSalmon.R R/xenome.R R/xenomeIndex.R README.md

docker4seq_devel.Rproj

docs/404.html

docs/CONTRIBUTING.html

docs/LICENSE-text.html

docs/articles/casc.html

docs/articles/demonstrative_workflow.html

docs/articles/docker4seq.html

docs/articles/index.html

docs/articles/rsconnect/documents/casc.html

docs/articles/rsconnect/documents/demonstrative_workflow.html

docs/articles/rsconnect/documents/docker4seq.html

docs/articles/rsconnect/documents/skeleton.html

docs/articles/rsconnect/documents/supplementary_data.html

docs/articles/skeleton.html

docs/articles/supplementary_data.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/inst/img/chipseq0.jpeg

docs/inst/img/chipseq1.jpeg

docs/inst/img/chipseq3.jpeg

docs/inst/img/chipseq_performance_bis.jpg

docs/inst/img/counts1.jpeg

docs/inst/img/counts2.jpeg

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docs/inst/img/de1.jpeg

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docs/inst/img/es.jpeg

docs/inst/img/expp1.jpeg

docs/inst/img/filtercounts.jpeg

docs/inst/img/mirna1.jpeg

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docs/inst/img/mirna_covars.jpeg

docs/inst/img/mirnaseq_performance_bis.jpg

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docs/inst/img/pca1.jpeg

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docs/inst/img/rnaseq1.jpeg

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docs/inst/img/rnaseq7.jpeg

docs/inst/img/salmonCounts.jpeg

docs/inst/img/salmonIndex.jpeg

docs/inst/img/salmon_rsem.jpg

docs/inst/img/samplesize1.jpeg

docs/inst/img/silhouette.stability.jpg

docs/inst/img/ss.jpeg

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docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/CIRCexplorer2.html

docs/reference/Rplot001.png

docs/reference/annoByGtfchipseq.html

docs/reference/anovaLike.html

docs/reference/bowtie2.html

docs/reference/bowtie2Index.html

docs/reference/bwa.html

docs/reference/bwaIndex.html

docs/reference/bwaIndexUcsc.html

docs/reference/cdhit.html

docs/reference/chipseq.html

docs/reference/chipseqCounts.html

docs/reference/circrnaAnnotations.html

docs/reference/circrnaBSJunctions.html

docs/reference/circrnaClassification.html

docs/reference/circrnaMergePredictions.html

docs/reference/circrnaOverlapResults.html

docs/reference/circrnaPrepareFiles.html

docs/reference/circrnaQuantification.html

docs/reference/circrnaReformat.html

docs/reference/ciri2.html

docs/reference/ciriAS.html

docs/reference/cutadapt.html

docs/reference/deeptoolBwig.html

docs/reference/demultiplexing.html

docs/reference/dockerTest.html

docs/reference/downloadContainers.html

docs/reference/experimentPower.html

docs/reference/fastq2fasta.html

docs/reference/fastqc.html

docs/reference/filterCounts.html

docs/reference/gatkDNA.html

docs/reference/getInfo.html

docs/reference/hashclone.html

docs/reference/heatmapBase.html

docs/reference/heatmaply.html

docs/reference/index.html

docs/reference/kraken.html

docs/reference/macs2.html

docs/reference/mergeData.html

docs/reference/mirnaCounts.html

docs/reference/mirnaCovar.html

docs/reference/multiQC.html

docs/reference/oncosnp.html

docs/reference/oncosnpAnnotation.html

docs/reference/pca.html

docs/reference/platypus.html

docs/reference/platypusFilter.html

docs/reference/prepare4expands.html

docs/reference/pubmedNet.html

docs/reference/rnaseqCounts.html

docs/reference/rsemBw.html

docs/reference/rsemanno.html

docs/reference/rsemannoByGtf.html

docs/reference/rsemstar.html

docs/reference/rsemstarIndex.html

docs/reference/rsemstarUscsIndex.html

docs/reference/runDocker.html

docs/reference/salmonAnnotation.html

docs/reference/salmonCounts.html

docs/reference/salmonIndex.html

docs/reference/sample2experiment.html

docs/reference/sampleSize.html

docs/reference/skeleton.html

docs/reference/skewer.html

docs/reference/skewerXSergio.html

docs/reference/sncRNA.html

docs/reference/snvPreprocessing.html

docs/reference/sraDownload.html

docs/reference/star.html

docs/reference/star2steps.html

docs/reference/starChimeric.html

docs/reference/starChipIndex.html

docs/reference/starchipCircle.html

docs/reference/testSeqbox.html

docs/reference/trimFasta.html

docs/reference/wrapperCiri.html

docs/reference/wrapperDeseq2.html

docs/reference/wrapperPdx.html

docs/reference/wrapperSTARChip.html

docs/reference/wrapperSalmon.html

docs/reference/xenome.html

docs/reference/xenomeIndex.html

docs/sitemap.xml

docs/supplementary_data.html

docs/vignettes/docker4seq.R

docs/vignettes/docker4seq.html

docs/vignettes/docker4seq.md docs/vignettes/skeleton.R

docs/vignettes/skeleton.html

docs/vignettes/skeleton.md

inst/.DS_Store

inst/containers/chipseq.txt

inst/containers/containers.txt

inst/containers/containersNames.txt

inst/containers/ncrna.txt

inst/containers/rnaseq.txt

inst/examples/4t1_counts.txt

inst/examples/SampleSheet.csv

inst/examples/arraycnvoutput.txt.zip

inst/examples/cnv1.cnvs

inst/examples/mb231_counts.txt

inst/examples/platypus.txt

inst/examples/readme.txt

inst/extras/indrop.yaml

inst/extras/starchip-circles.params

inst/extras/starchip-circles.params.txt

inst/extras/xeno_script.py

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/docker4seq_logo.png

inst/img/es.jpeg

inst/img/expp1.jpeg

inst/img/filtercounts.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/CIRCexplorer2.Rd man/annoByGtfchipseq.Rd man/anovaLike.Rd man/bowtie2.Rd man/bowtie2Index.Rd man/bwa.Rd man/bwaIndex.Rd man/bwaIndexUcsc.Rd man/cdhit.Rd man/chipseq.Rd man/chipseqCounts.Rd man/circrnaAnnotations.Rd man/circrnaBSJunctions.Rd man/circrnaClassification.Rd man/circrnaMergePredictions.Rd man/circrnaOverlapResults.Rd man/circrnaPrepareFiles.Rd man/circrnaQuantification.Rd man/circrnaReformat.Rd man/ciri2.Rd man/ciriAS.Rd man/cutadapt.Rd man/deeptoolBwig.Rd man/demultiplexing.Rd man/dockerTest.Rd man/downloadContainers.Rd man/experimentPower.Rd man/fastq2fasta.Rd man/fastqc.Rd man/filterCounts.Rd man/gatkDNA.Rd man/getInfo.Rd man/hashclone.Rd man/heatmapBase.Rd man/heatmaply.Rd man/kraken.Rd man/macs2.Rd man/mergeData.Rd man/mirnaCounts.Rd man/mirnaCovar.Rd man/multiQC.Rd man/oncosnp.Rd man/oncosnpAnnotation.Rd man/pca.Rd man/platypus.Rd man/platypusFilter.Rd man/prepare4expands.Rd man/pubmedNet.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/skeleton.Rd man/skewer.Rd man/skewerXSergio.Rd man/sncRNA.Rd man/snvPreprocessing.Rd man/sraDownload.Rd man/star.Rd man/star2steps.Rd man/starChimeric.Rd man/starChipIndex.Rd man/starchipCircle.Rd man/testSeqbox.Rd man/trimFasta.Rd man/wrapperCiri.Rd man/wrapperDeseq2.Rd man/wrapperPdx.Rd man/wrapperSTARChip.Rd man/wrapperSalmon.Rd man/xenome.Rd man/xenomeIndex.Rd

supplementary_data.html

supplementary_data.md

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.

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

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

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

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

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

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