Files in jmw86069/jambio

Analysis and Visualization of Gene Splice Variants and Transcriptome Data

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/jam-sets.R R/jambio-data.R R/jambio-design.R R/jambio-gg.R R/jambio-gtf.R R/jambio-import.R R/jambio-plot.R R/jambio-tx.R R/splicejam-geoms.R R/splicejam-plots.R R/splicejam-shiny-constants.R R/splicejam-shiny-data.R R/splicejam-shiny-server.R R/splicejam-shiny-ui.R R/splicejam-shiny.R README.Rmd README.md TODO.md TODO_SGSeq_notes.md TODO_shiny_opt.md

_pkgdown.yml

data/demodata.rda

data/test_cov_gr.rda

data/test_cov_wide_gr.rda

data/test_exon_gr.rda

data/test_exon_wide_gr.rda

data/test_junc_gr.rda

data/test_junc_wide_gr.rda

docs/404.html

docs/TODO.html

docs/articles/basic-rnaseq-workflow.html

docs/articles/basic-rnaseq-workflow_files/figure-html/jammaplot_counts-1.png

docs/articles/basic-rnaseq-workflow_files/figure-html/jammaplot_tpm-1.png

docs/articles/basic-rnaseq-workflow_files/figure-html/tpm_counts-1.png

docs/articles/basic-rnaseq-workflow_files/header-attrs-2.1/header-attrs.js

docs/articles/create-a-sashimi-plot.html

docs/articles/create-a-sashimi-plot_files/figure-html/compress_intron_cov-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/cov_plots-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/gene_plot-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/gene_plot-2.png

docs/articles/create-a-sashimi-plot_files/figure-html/gene_plot-3.png

docs/articles/create-a-sashimi-plot_files/figure-html/gene_plot-4.png

docs/articles/create-a-sashimi-plot_files/figure-html/plot_sashimi-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/plot_sashimi_exons-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/plot_sashimi_gr-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/plot_sashimi_wide-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/plot_test_junc-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/zoom_gria1-1.png

docs/articles/create-a-sashimi-plot_files/figure-html/zoom_sashimi-1.png

docs/articles/create-a-sashimi-plot_files/header-attrs-2.1/header-attrs.js

docs/articles/create-a-sashimi-plot_files/header-attrs-2.9/header-attrs.js

docs/articles/index.html

docs/articles/shiny-server-for-sashimi-plots.html

docs/articles/shiny-server-for-sashimi-plots_files/header-attrs-2.9/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/Rplot003.png

docs/reference/Rplot004.png

docs/reference/Rplot005.png

docs/reference/addGRLgaps.html

docs/reference/addGRgaps.html

docs/reference/ale2violin.html

docs/reference/annotateGRLfromGRL.html

docs/reference/annotateGRfromGR.html

docs/reference/assignGRLexonNames.html

docs/reference/bgaPlotly3d.html

docs/reference/closestExonToJunctions.html

docs/reference/codonUsage2df.html

docs/reference/combineGRcoverage.html

docs/reference/compressPolygonM.html

docs/reference/curateDFtoDF.html

docs/reference/curateVtoDF.html

docs/reference/defineDetectedTx.html

docs/reference/detectedTxInfo.html

docs/reference/df2colorSub-1.png

docs/reference/df2colorSub-2.png

docs/reference/df2colorSub.html

docs/reference/dfWide2segments.html

docs/reference/dna2codon.html

docs/reference/escapeWhitespaceRegexp.html

docs/reference/exoncov2polygon-1.png

docs/reference/exoncov2polygon.html

docs/reference/factor2label.html

docs/reference/figures/README-gria1_sashimi-1.png

docs/reference/figures/README-gria1_sashimi_zoom-1.png

docs/reference/figures/mouse_hippocampus.png

docs/reference/figures/splicejam_logo.png

docs/reference/findOverlapsGRL.html

docs/reference/flattenExonsBy.html

docs/reference/flattenExonsByGene.html

docs/reference/gene2gg-1.png

docs/reference/gene2gg-2.png

docs/reference/gene2gg-3.png

docs/reference/gene2gg.html

docs/reference/geom_diagonal_wide_arc-1.png

docs/reference/geom_diagonal_wide_arc-2.png

docs/reference/geom_diagonal_wide_arc-3.png

docs/reference/geom_diagonal_wide_arc.html

docs/reference/geomean.html

docs/reference/getFirstStrandedFromGRL.html

docs/reference/getGRLgaps.html

docs/reference/getGRcoverageFromBw.html

docs/reference/getGRgaps.html

docs/reference/get_fn_envir.html

docs/reference/grl2df-1.png

docs/reference/grl2df-2.png

docs/reference/grl2df-3.png

docs/reference/grl2df-4.png

docs/reference/grl2df.html

docs/reference/groups2contrasts.html

docs/reference/import_juncs_from_bed.html

docs/reference/index.html

docs/reference/intercalate.html

docs/reference/internal_junc_score.html

docs/reference/jamCai.html

docs/reference/jamGeomean.html

docs/reference/jam_isDisjoint.html

docs/reference/jitter_norm.html

docs/reference/launchSashimiApp.html

docs/reference/list2im.html

docs/reference/makeTx2geneFromGtf.html

docs/reference/make_ref2compressed-1.png

docs/reference/make_ref2compressed-2.png

docs/reference/make_ref2compressed.html

docs/reference/plotSashimi-1.png

docs/reference/plotSashimi.html

docs/reference/prepareSashimi-1.png

docs/reference/prepareSashimi.html

docs/reference/psl2df.html

docs/reference/runDiffSplice.html

docs/reference/sashimiAppConstants.html

docs/reference/sashimiAppServer.html

docs/reference/sashimiAppUI.html

docs/reference/sashimiDataConstants.html

docs/reference/shrinkMatrix.html

docs/reference/simplifyXY-1.png

docs/reference/simplifyXY.html

docs/reference/sortGRL.html

docs/reference/sortSamples.html

docs/reference/spliceGR2junctionDF.html

docs/reference/splicejam-extensions.html

docs/reference/spline3d.html

docs/reference/stackJunctions-1.png

docs/reference/stackJunctions-2.png

docs/reference/stackJunctions-3.png

docs/reference/stackJunctions-4.png

docs/reference/stackJunctions-5.png

docs/reference/stackJunctions.html

docs/reference/strsplitOrdered.html

docs/reference/test_cov_gr-1.png

docs/reference/test_cov_gr-2.png

docs/reference/test_cov_gr.html

docs/reference/test_cov_wide_gr-1.png

docs/reference/test_cov_wide_gr-2.png

docs/reference/test_cov_wide_gr-3.png

docs/reference/test_cov_wide_gr.html

docs/reference/test_exon_gr-1.png

docs/reference/test_exon_gr.html

docs/reference/test_exon_wide_gr-1.png

docs/reference/test_exon_wide_gr-2.png

docs/reference/test_exon_wide_gr.html

docs/reference/test_junc_gr-1.png

docs/reference/test_junc_gr.html

docs/reference/test_junc_wide_gr-1.png

docs/reference/test_junc_wide_gr-2.png

docs/reference/test_junc_wide_gr-3.png

docs/reference/test_junc_wide_gr.html

docs/reference/to_basic.GeomShape.html

docs/reference/tx2ale.html

inst/extdata/Mouse_codon_usage.txt

man/addGRLgaps.Rd man/addGRgaps.Rd man/ale2violin.Rd man/annotateGRLfromGRL.Rd man/annotateGRfromGR.Rd man/assignGRLexonNames.Rd man/bgaPlotly3d.Rd man/closestExonToJunctions.Rd man/codonUsage2df.Rd man/combineGRcoverage.Rd man/compressPolygonM.Rd man/curateDFtoDF.Rd man/curateVtoDF.Rd man/defineDetectedTx.Rd man/describeGtfAttrNames.Rd man/detectedTxInfo.Rd man/df2colorSub.Rd man/dfWide2segments.Rd man/dna2codon.Rd man/escapeWhitespaceRegexp.Rd man/exoncov2polygon.Rd man/factor2label.Rd

man/figures/README-gria1_sashimi-1.png

man/figures/README-gria1_sashimi_zoom-1.png

man/figures/mouse_hippocampus.png

man/figures/splicejam_logo.png

man/findOverlapsGRL.Rd man/flattenExonsBy.Rd man/gene2gg.Rd man/geom_diagonal_wide_arc.Rd man/geomean.Rd man/getFirstStrandedFromGRL.Rd man/getGRLgaps.Rd man/getGRcoverageFromBw.Rd man/getGRgaps.Rd man/get_fn_envir.Rd man/grl2df.Rd man/groups2contrasts.Rd man/import_juncs_from_bed.Rd man/intercalate.Rd man/internal_junc_score.Rd man/jamCai.Rd man/jamGeomean.Rd man/jam_isDisjoint.Rd man/jitter_norm.Rd man/launchSashimiApp.Rd man/list2im.Rd man/makeTx2geneFromGtf.Rd man/make_ref2compressed.Rd man/plotSashimi.Rd man/prepareSashimi.Rd man/psl2df.Rd man/readGtf.Rd man/runDiffSplice.Rd man/sashimiAppConstants.Rd man/sashimiAppServer.Rd man/sashimiAppUI.Rd man/sashimiDataConstants.Rd man/shrinkMatrix.Rd man/simplifyXY.Rd man/sortGRL.Rd man/sortSamples.Rd man/spliceGR2junctionDF.Rd man/splicejam-extensions.Rd man/spline3d.Rd man/stackJunctions.Rd man/strsplitOrdered.Rd man/test_cov_gr.Rd man/test_cov_wide_gr.Rd man/test_exon_gr.Rd man/test_exon_wide_gr.Rd man/test_junc_gr.Rd man/test_junc_wide_gr.Rd man/to_basic.GeomShape.Rd man/tx2ale.Rd

splicejam.Rproj

splicejam_shiny_deps.md

vignettes/.gitignore

vignettes/basic-rnaseq-workflow.Rmd vignettes/create-a-sashimi-plot.Rmd vignettes/shiny-server-for-sashimi-plots.Rmd

jmw86069/jambio documentation built on April 21, 2024, 2:48 p.m.