5855fd18cc7147c5f1e0453d94287e3b *DESCRIPTION
10bf23b31c10a47cfe88540e8ac82f65 *NAMESPACE
1d2d9c6cae884b950dbafd6e28188567 *NEWS.md
2990b45272c12ac4e764c24fcbb68fd0 *R/VISTA-class.R
f0d5e962bd361415e50244ea2209fe98 *R/VISTA-package.R
f012dc8cd7beac71de275b6a3af32544 *R/accessors.R
2d7840c8ae735149060d9255563a8cdc *R/benchmarking.R
a4d6a8423b3cd4ef9e2042ccc70981c0 *R/bioccheck_roxygen_fixes.R
40fb06ea33a11fd1e61ea0827d2931d3 *R/counts-methods.R
ea23a3f04f261c80fe1e9c1dcabe781d *R/data-documentation.R
3b55be81f721e20c4602bf35a62806d0 *R/deconv.R
0903eb4a93fa35674b7ad95044f96a1f *R/defaults.R
4c31aac04d22e9dc123fd7e90766ab75 *R/deprecation.R
f2a0100560614c01f23ab832d058b132 *R/example_vista.R
7ee8f86d3fbd4886ca90f5013eef31c1 *R/exporting.R
a2836f5c33a6b66993a8ea0a6aa6b9f0 *R/functional_analysis.R
25567ccdd8ac9da27b8edf8ce7418df9 *R/input_preparation.R
6f19f689cc06d44374f39d66518b8258 *R/print.R
48b2de49aca266b08b32cb50349b4706 *R/reporting.R
2d5dbf6feb248dda79632b5326c2baa8 *R/rnaseq_related.R
2feeca30aba6400c4dc7441619859352 *R/show-methods.R
a684c7a0fb09cf43008ca1749ef8bc9b *R/subset-methods.R
75b47c2105f1cf2c0c6c20d26ba61f76 *R/sysdata.rda
a716c8db58c39d0c83d5be1c66f956cb *R/updateObject.R
2e5d06c393ae7566c383996c94b92a46 *R/utils-internal.R
f4f87fb570955dd5561602cdd64df6ba *R/validate.R
d726bc87d52a9092c6ade39503b7e540 *R/viz_related.R
52e798025b8d75adcc9a9dae000ac969 *README.md
10639005a4d7d0fc4f6bfe20c63fd957 *build/vignette.rds
4a7c43a9aa2f64c278ffe4bac06c122a *data/count_data.rda
200fe0c696e97b60acaed3fa6701fdbe *data/sample_metadata.rda
bca1db23480e24c56483a29360346d6b *inst/benchmarks/benchmark-de-equivalence.R
36978388febac3574b04bd6e0d224a3f *inst/doc/VISTA-airway.R
dba7d47061555eb85d7caa9d1df17b54 *inst/doc/VISTA-airway.Rmd
7a1675359b4e405cdefa40e4562c1422 *inst/doc/VISTA-airway.html
cc69ca1b93672319aa76b2d194c885db *inst/reports/vista-report-template.yml
30b1d7a509a51d79aa52f4a9b2fd898b *man/VISTA-accessors.Rd
2bb8c2e7a4a951c60b071a72be8afd91 *man/VISTA-class.Rd
cfe3d662722ae19f129f88d1276940e5 *man/VISTA-deprecated.Rd
0099327ac0bff5cae3435882eebd6eb7 *man/VISTA-package.Rd
316fd3be21c33fc8421d566891a5dee1 *man/VISTA-show.Rd
bebbb2aec7073c7cf909f94f01e166c3 *man/VISTA-subset.Rd
527906759af4779f6a2308152b09612d *man/as_deseq_dataset.Rd
cab8a0912745cc185d20b800e4d1a759 *man/as_vista.Rd
47eed9bfe247ca836fe9297f4bd43417 *man/benchmark_vista_equivalence.Rd
040797d1246984fed738a584075eacb2 *man/count_data.Rd
c3f3756167352ce322c57c5a754e26f4 *man/counts.Rd
80867e3ebbdd5f0f8030221871cdcaa5 *man/create_vista.Rd
1dee9c2b1c1e1d0eb20bfbed35b28d00 *man/derive_vista_metadata.Rd
6dc8d4bd3042ed65ec56008a6f5a3beb *man/dot-EnhancedVolcano2.Rd
4a1ecbe1c53a5c031fc9d40a06d6e485 *man/dot-align_de_to_counts.Rd
8815a986f93f63f5a7f7be678fee657a *man/dot-categorize_deg_results.Rd
56756e475b5aa71db763a81b9f44bc29 *man/dot-prepare_pca_dataframe.Rd
385d8ec0dc68beed91966419c108e394 *man/dot-run_deseq_comparisons.Rd
828741a4ec06ca12f855640773b571f1 *man/dot-tidy_de_results.Rd
a57f5cfe00fa7d6da1a45aaf421a68d5 *man/enrichMsigDB.Rd
cba220d27b2fa81827fd9a147eee1f9d *man/example_vista.Rd
f1099afc53f93e295d640ab27e275a02 *man/export_vista_assets.Rd
9eadd020c53305c03e407eb5138ea1e2 *man/figures/logo.png
7a2345e2a36d1978c93490c1ffdb5987 *man/get_cell_fractions.Rd
da5909b5b9405825bfc3bea82a8ad130 *man/get_celltype_barplot.Rd
11666a130e596e4b22dcd63bee24b0cc *man/get_celltype_group_dotplot.Rd
0c799f887061b1160b6dce6d7dfaa3a1 *man/get_celltype_heatmap.Rd
eb2409c658c981546f1e0d56263d2cdc *man/get_chromosome_plot.Rd
a03bf0bdb9c2a02d0c7c9ad8e0b1b504 *man/get_corr_heatmap.Rd
1316e7400a9e961e94cd464f9f05e60f *man/get_deg_alluvial.Rd
9b2796ecfc69c443a8c51f81bdbffa7a *man/get_deg_count_barplot.Rd
49e54e8b7c6ab187b6867161bca586c1 *man/get_deg_count_donutplot.Rd
ae7f8bb9a97ca41105c9f4547e884b1f *man/get_deg_count_pieplot.Rd
7e54f96c66510e733db093247f31163e *man/get_deg_venn_diagram.Rd
c7367885c56f8ee05ba6870191117c90 *man/get_enrichment_chord.Rd
7fe87b7f75bd8245d68fdef060a89a95 *man/get_enrichment_plot.Rd
7da685e022636828ed348283aaaf6c8b *man/get_expression_barplot.Rd
dd2fcd3e62ec7e4fe7c1ddd4526f8786 *man/get_expression_boxplot.Rd
ed49b742120cd1da5982e7c16a71cba1 *man/get_expression_chromosome_plot.Rd
b6b31c4f4415150cdd0486d7dff18b7e *man/get_expression_density.Rd
8c099c43b7bbffd71ae8266e5f75ce6c *man/get_expression_heatmap.Rd
c689ff408c476ea30fad65caa0fc8207 *man/get_expression_joyplot.Rd
cbed8c04c26389925ca8cd3caf635e34 *man/get_expression_lineplot.Rd
e6e3a450a4761684ced0dcac0629737d *man/get_expression_lollipop.Rd
7c35cd923ac86bfb0365c7e97e6230a4 *man/get_expression_matrix.Rd
507184b31bb1a05ae8732f99c4204434 *man/get_expression_raincloud.Rd
6c498c9febbf4bd0a5754558bb4f6f52 *man/get_expression_scatter.Rd
bb06857a5b6b27f8b14b43e4237ee5c0 *man/get_expression_violinplot.Rd
93a56b7c02cb740c093c614009b3838b *man/get_foldchange_barplot.Rd
50f01d3d6fe13bbce8c22c11b13ac4dd *man/get_foldchange_boxplot.Rd
b66a340f836c20e644c7fc53ead99415 *man/get_foldchange_chromosome_plot.Rd
66e0d1ac7005575ed49e0e58b27cd1dd *man/get_foldchange_heatmap.Rd
189cc3693335ab3648e2de844a8df586 *man/get_foldchange_lineplot.Rd
5d3458b72d74f6b6953aeba16ea31da6 *man/get_foldchange_lollipop.Rd
03da593ffed8652345d2ee78b4894ffe *man/get_foldchange_matrix.Rd
35c3f4d336ff41817edb2a802c4b6edc *man/get_foldchange_raincloud.Rd
a20dc29c9a7ae73331f629bd4dd30e29 *man/get_foldchange_scatter.Rd
55f94e8a8acfaa0c232de4aaf0e15939 *man/get_genes_by_regulation.Rd
d32dfe2f08b8e738b2fc6709939cea84 *man/get_go_enrichment.Rd
df8e793d23d40c52957365a85645aad2 *man/get_gsea.Rd
3cbe773c24b746fa5765c745cb9cc3ae *man/get_kegg_enrichment.Rd
3cfd2488b8587c32cd79bcd0ef2ad5d5 *man/get_ma_plot.Rd
55277c81018493ca901c8679f21fe213 *man/get_mds_plot.Rd
653ac51eccd836da7b281626b923bbae *man/get_msigdb_enrichment.Rd
e1968f3fe32c99e36dda4ad898db614a *man/get_pairwise_corr_plot.Rd
1861698aa7b4ecbefa87f2899a1c8e0b *man/get_pathway_genes.Rd
f09a076bb1773074a678246fe5821477 *man/get_pathway_heatmap.Rd
124ea2659dbe0a31915c498f4cac0f19 *man/get_pca_plot.Rd
11fd5e94c2091d9e82876bc753bdc941 *man/get_umap_plot.Rd
3147bcb64de8de7467e46a063563d441 *man/get_volcano_plot.Rd
cf891e4eb1ff192dc516ea96dd57d057 *man/match_vista_inputs.Rd
32fb832c11ccfefc2fed7c04a805cf74 *man/print.VISTA.Rd
5cf763ed616b12815352065299872e69 *man/read_vista_counts.Rd
166f9508505e0b2cda40db3c0b7cc665 *man/read_vista_metadata.Rd
8bfdb8c22771e7bbcb76a3c6dcb38253 *man/run_cell_deconvolution.Rd
d27a627184f1a8c51c48071a785f043e *man/run_deseq_analysis.Rd
480f6e1d937f8577876197d988468853 *man/run_vista_report.Rd
e49c518d08851b53a51ac31a608c9793 *man/sample_metadata.Rd
83d1053ae7e021261be019d422c02fc0 *man/save_vista_data.Rd
fe9bb4c88b6a61a653149a0aff8ddd8f *man/save_vista_plot.Rd
3b388ba897fd3a64277220d1ee8d56bf *man/set_de_source.Rd
4cf8d1d6a8823d7b1ef5b3131727bb9b *man/set_rowdata.Rd
fad7b47637a2c50389bba8cc30584dcb *man/set_vista_comparison_colors.Rd
23aa98a3aaced18862d8ec8132073c1d *man/set_vista_group_colors.Rd
9b48f03951f32cddec188d34d294a6c8 *man/updateObject-VISTA-method.Rd
a2991937d4ef1a899f34f9caae2e94a6 *man/validate_vista.Rd
a28ae516d11982f711e10af6557b5b7f *man/validate_vista_deep.Rd
d89cc2c8a1c9b336d99ca08303a8bc87 *tests/testthat.R
fa2269890d94b8ed647de26b3a902441 *tests/testthat/_snaps/plot-stability.md
fdfa7dad4bd6c8549ec0f0b5bb78dce1 *tests/testthat/helper-data.R
2d12185754453ff426775f3437248627 *tests/testthat/test-accessors.R
73456aed3262565aa2eb034c9db5b623 *tests/testthat/test-align-de-to-counts.R
0a4e4a7ba4c754a35a00314277996839 *tests/testthat/test-api-dots.R
c2ca5ec191fcb756fccb8272e36dff9c *tests/testthat/test-benchmarking.R
3eba2abbb9cde79e63f3fe8b9cdc9f74 *tests/testthat/test-class-print-reporting.R
efe201bbd9bad86391fbca240b1b7776 *tests/testthat/test-create-vista.R
a5afac78f4d44fce8253e46ff648f464 *tests/testthat/test-cutoff-consistency.R
5a26c84e9c54d08121a65a249988ccc8 *tests/testthat/test-deconvolution.R
79684dc345acba4b9c54f84928cc975b *tests/testthat/test-deprecation-registry.R
1e584dbb5a297d3ec7a3ff25f9b6ce4e *tests/testthat/test-enrichment.R
0ebc0315a7642f4ccfd539a8614c6761 *tests/testthat/test-example-vista.R
56455c8a2fe9245c3c85a7e4992b476c *tests/testthat/test-exporting.R
f03aec12e552c087f15f540518e5031b *tests/testthat/test-expression-matrix-order.R
5780730e50553e52900be3a668ecf1fc *tests/testthat/test-expression-plots.R
d8c5e7b908e790a435f9d8ca5dc43467 *tests/testthat/test-foldchange-plots.R
df8829c8cc47a03abadcea58c6c1b660 *tests/testthat/test-foldchange-scatter.R
f97d3f6f28a3b1b5172fbb67941ce2f2 *tests/testthat/test-harmonization-gaps.R
efe4a68ecf0c5fba6003c5662521e6ec *tests/testthat/test-heatmap-display.R
e84286b3bf3d89c2b1d9ee28f76df309 *tests/testthat/test-input-preparation.R
e3031077823790df5e3a642587f24678 *tests/testthat/test-label-value-integrity.R
5f7df3d1afa11cfadf9010b8a10ff241 *tests/testthat/test-order-independence.R
fa6eef6038d7fc5d448fedf3ce143b8f *tests/testthat/test-plot-stability.R
669eb1aa62a060b79748ebb1c7736a3f *tests/testthat/test-pvalue-labels.R
a79a5aae42bdfbb5bb516f2c00d895f8 *tests/testthat/test-raw-counts.R
7df4e3077afbc9b95abd8651c38295c7 *tests/testthat/test-return-type.R
a68cafe49ae5ad641431b1650d3325a5 *tests/testthat/test-rowdata.R
9b7e5564340c03bdf59d2b699df0c833 *tests/testthat/test-subsetting.R
e79ef5d4f7d7a50ab25568a54fc4a8cb *tests/testthat/test-untested-exports.R
06b111427c2364be55facce684a615b9 *tests/testthat/test-validation.R
04011726068b63d6624c501a3452ae0f *tests/testthat/test-visualization-advanced.R
dba7d47061555eb85d7caa9d1df17b54 *vignettes/VISTA-airway.Rmd
