Files in lpantano/bcbioSmallRna
small RNA-Seq Utilities
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/AllClasses.R
R/AllGenerics.R
R/AllMethods.R
R/bcbioSmallRna.R
R/dataset.R
R/download.R
R/internal-project_dir.R
R/internal-smallrna.R
R/internal-yaml.R
R/loadRun.R
R/plots-smallrna.R
R/reexport.R
README.md
bcbioSmallRna.Rproj
data-raw/sbcb.R
data/sbcb.rda
docs/LICENSE-text.html
docs/LICENSE.html
docs/articles/browsing-object.html
docs/articles/browsing_object.html
docs/articles/index.html
docs/articles/qc-example.html
docs/articles/qc-example_files/figure-html/adapter-1.png
docs/articles/qc-example_files/figure-html/adapter-size-dist-1.png
docs/articles/qc-example_files/figure-html/cluster-heatmap-1.png
docs/articles/qc-example_files/figure-html/cluster-pca-1.png
docs/articles/qc-example_files/figure-html/isomiRs-1.png
docs/articles/qc-example_files/figure-html/mirna-heatmap-1.png
docs/articles/qc-example_files/figure-html/mirna-pca-1.png
docs/articles/qc-example_files/figure-html/plot_mirna_counts-1.png
docs/articles/qc-example_files/figure-html/plot_srna_clusters-1.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/downloads/_footer.Rmd
docs/downloads/_header.Rmd
docs/downloads/_output.yaml
docs/downloads/index.html
docs/downloads/setup.R
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/_footer.Rmd
docs/reference/_header.Rmd
docs/reference/_output.yaml
docs/reference/adapter.html
docs/reference/bcbio.html
docs/reference/bcbioSmallRna-package.html
docs/reference/bcbioSmallRnaDataSet.html
docs/reference/data_versions.html
docs/reference/download.html
docs/reference/index.html
docs/reference/loadSmallRnaRun.html
docs/reference/metrics.html
docs/reference/mirna.html
docs/reference/plots-smallrna-1.png
docs/reference/plots-smallrna-2.png
docs/reference/plots-smallrna-3.png
docs/reference/plots-smallrna-4.png
docs/reference/plots-smallrna-5.png
docs/reference/plots-smallrna-6.png
docs/reference/plots-smallrna.html
docs/reference/plotsSmallPCA.html
docs/reference/program_versions.html
docs/reference/reexports.html
docs/reference/sbcb.html
docs/reference/setup.R
inst/extra/E-GEUV-2.sdrf.txt
inst/extra/PRJEB3365.txt
inst/extra/geu_tiny.csv
inst/extra/geu_tiny/config/geu_tiny-template.yaml
inst/extra/geu_tiny/config/geu_tiny.csv
inst/extra/geu_tiny/config/geu_tiny.yaml
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/bcbio-nextgen-commands.log
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/bcbio-nextgen.log
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/counts.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/counts_mirna.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/data_versions.csv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/metadata.csv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/list_files.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/list_files_final.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_config.yaml
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc.log
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_bcbio_metrics.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_data.json
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_data_final.json
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_fastqc.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_general_stats.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_samtools_idxstats.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_samtools_stats.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/multiqc_sources.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/seqbuster_isomirs.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_data/seqbuster_mirs.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/multiqc_report.html
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Per_base_N_content.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Per_base_sequence_content.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Per_base_sequence_quality.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Per_sequence_GC_content.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Per_sequence_quality_scores.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Sequence_Duplication_Levels.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/fastqc/Sequence_Length_Distribution.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185036_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185068_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185082_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185102_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185125_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185252_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185400_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185403_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185470_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/multiqc/report/metrics/ERS185473_bcbio.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/programs.txt
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/project-summary.yaml
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/counts.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/counts_sequence.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/log/460.bed
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/log/482.bed
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/log/run.log
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/log/trace.log
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/positions.bed
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/read_stats.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/seqs_rmlw.bam_cov.tsv
inst/extra/geu_tiny/final/2018-12-05_geu_tiny/seqcluster/size_counts.tsv
inst/extra/geu_tiny/final/ERS185036/ERS185036-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185036/ERS185036-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185068/ERS185068-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185068/ERS185068-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185082/ERS185082-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185082/ERS185082-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185102/ERS185102-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185102/ERS185102-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185125/ERS185125-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185125/ERS185125-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185252/ERS185252-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185252/ERS185252-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185400/ERS185400-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185400/ERS185400-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185403/ERS185403-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185403/ERS185403-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185470/ERS185470-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185470/ERS185470-ready.trimming_stats
inst/extra/geu_tiny/final/ERS185473/ERS185473-mirbase-ready.counts
inst/extra/geu_tiny/final/ERS185473/ERS185473-ready.trimming_stats
inst/rmarkdown/templates/srnaseq/skeleton/skeleton.Rmd
inst/rmarkdown/templates/srnaseq/template.yaml
inst/sticker/bcbioSmallRna.png
inst/sticker/logo.png
inst/sticker/sticker.R
man/adapter.Rd
man/bcbio.Rd
man/bcbioSmallRna-package.Rd
man/bcbioSmallRnaDataSet.Rd
man/data_versions.Rd
man/download.Rd
man/loadSmallRnaRun.Rd
man/metrics.Rd
man/mirna.Rd
man/plots-smallrna.Rd
man/plotsSmallPCA.Rd
man/program_versions.Rd
man/reexports.Rd
man/sbcb.Rd
tests/testthat.R
tests/testthat/report/sbcb.rda
tests/testthat/test_template.R
vignettes/browsing-object.Rmd
vignettes/qc-example.Rmd
