add_pathways | Pathway Alterations |
add.perc | Add a percentage to counts |
annotate_any_panel | Annotate Missing Gene Values According to Specifi Panels |
annotate_specific_panel | Utility function to insert NA's According to Panel |
check_cna_input | Check CNA data frame to ensure columns are correct |
check_fusion_input | Check fusion data frame to ensure columns are correct |
check_mutation_input | Checks MAF input to ensure column names are correct and... |
clin.patients | An example of clinical patient level information file from... |
clin.sample | An example of clinical sample level information file from... |
cna | An example copy number alteration raw calls file from IMPACT... |
CNregions.mod | CNregions.mod Modified CNregions function from the facets... |
create_gene_binary | Enables creation of a binary matrix from a mutation file with... |
curated_genes | List of curated genes for IMPACT oncoKB annotation. |
dat_oncoprint | Enables creation of a matrix used to generate an OncoPrint... |
dot-cna_gene_binary | Make Binary Matrix From CNA data frame |
dot-fusions_gene_binary | Make Binary Matrix From Fusion data frame |
dot-mutations_gene_binary | Make Binary Matrix From Mutation data frame |
dot-sum_alts_in_pathway | Title |
facets_dat | facets_dat |
facets_heatmap | facets_heatmap |
fusion | An example of fusions calls file from IMPACT cbioPortal... |
gene_panels | Public Gene Panels on cBioPortal |
genie_gene_info | GENIE consortium Gene Meta Data |
ggcomut | Comutation Heatmap of the Top Altered Genes |
gggenecor | Correlation Heatmap of the Top Altered Genes |
ggheatmap | Heatmap of all events after gene_binary - using binary... |
ggsamplevar | Histogram of Variants Per Sample Colored By Variant... |
ggsnvclass | Histogram of SNV class Counts |
ggtopgenes | Barplot of Most Frequently Altered Genes |
ggvarclass | Barplot of Variant Classification Counts |
ggvartype | Barplot of Variant Type Counts |
gnomer_colors | List of suggested color palettes for when you need a large... |
gnomer_cols | Function to extract colors from 'gnomer_colors' as hex codes |
gnomeR-package | gnomeR: Wrangle and analyze IMPACT and TCGA mutation data |
gnomer_pal | Return function to interpolate a gnomeR color palette |
gnomer_palette | Access the colors in a gnomeR color palette |
gnomer_palettes | Complete list of gnomeR color palettes |
impact_gene_info | IMPACT Gene Meta Data |
mut | An example maf file from IMPACT cbioPortal dataset |
mutation_viz | Creates a set of plot summarising a mutation file. |
oncokb | OncoKB annotate \ Enables oncokb annotation of MAF, fusions... |
panel_names | GENIE panel names as found in synapse data |
pathways | IMPACT Gene Pathways |
pipe | Pipe operator |
plot_oncoprint | Creates the OncoPrint corresponding to the inputted genetic... |
recode_alias | Recode Hugo Symbol Column |
reformat_cna | Reformat CNA from maf version to wide version |
resolve_alias | Resolve Hugo Symbol Names with Aliases |
scale_color_pancan | Color scale creator to add gnomeR colors in ggplot |
scale_fill_pancan | Fill scale creator to add gnomeR colors in ggplot |
seg | A segmentation file from the cbioPortal datasets |
specify_impact_panels | IMPACT Panel Annotation of NA's |
substrRight | Utility Function to Extract SNV |
summarize_by_gene | Simplify binary matrix to one column per gene that counts any... |
tbl_genomic | tbl_genomic |
tcga_genes | A vector of 19441 hugo symbols in TCGA |
tcga_samples | Data frame of all TCGA sample ids and their corresponding... |
ti_341 | Intervals sequenced in 341 panel |
ti_410 | Intervals sequenced in 410 panel |
ti_468 | Intervals sequenced in 468 panel |
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