affy_probe_to_gene_symbol | use hgu133a.db or hgu133plus2.db to convert from affymetrix... |
assign_label_cex | Adjust label cex based on its number |
cal_entropy | calculate entroyp |
centroid_classify | Classify samples based on the feed in centroids |
clean_iterNMF | Extract, cleanup, and merge iter_NMF results |
clust_by_hier | Clustering by hierarchical |
clust_silhouette | Calculate silhouette index between two data frame |
compare_group | Compare two groups assignment results |
compare_groups_stats | Calculate statistics comparing two clustering results |
comp_module_genelist | Compute module gene list |
connect_gap_modules | Loop through each of the modules and connect the adjacent... |
corModuleUI | Sample correlation plot |
cor_mtest | load predefined gene list files for heatmap |
create.brewer.color | Create brewer color |
create_centroid | Create centroid based on the grouping info |
create.manual.color | Manually specify coloring for provided groups |
def_net_module2 | Identify the the edge of the modules (blocks) within the net... |
def_net_modules | Identify the the edge of the modules (blocks) within the net... |
deseq_norm | Normalize data through DESeq size factor |
detect_genecnt_platform | Check rownames from data and auto detect which platform it is... |
ext_gene_function | Extract ensembl_id using gene symbol |
extract_data_by_mad | Extract data by MAD value |
extract_data_by_math | Extract data by 'math' operation |
gene_convert_human_to_mouse | Use biomaRT to convert human gene to mouse gene |
gene_convert_mouse_to_human | use biomaRT to convert mouse gene to human gene |
getcentroid | Get centroid from data frame |
get_ClaNC_group | Get ClaNA Group info |
heatmap.3 | Published version of heatmap.3, with more options |
hello | Hello, World! |
is.whole | Check whether it is a integer whole value |
iter_nmf | Run iterative NMF for K=2 until it cannot no longer separate... |
load_genelist | load predefined gene list files for heatmap |
load_geneset | load predefined gene set files for GSEA |
module_finder | Identify the modules in Data within co-expression network |
multiplot | Multiple plot function |
mutual_info_from_confmatrix | Calculate Mutual information from confusion matrix |
mutual_info_from_vector | calculate Mutual information from two vector |
myboxplot | Custom version of boxplot |
myd3Heatmap | Custom version of d3heatmap |
myfread.table | Use data.table for faster read.table |
myHeatmap.3 | A Cat Function |
myNMF | Function to run NMF with different options |
my.write.matrix | Own version of writing matrix output |
name_to_color | Convert name to color |
NetConnectivity | Identify the informative genes in Data with top high... |
nmf_estim_plot | Generate individual plot for estimating K |
nmf_extract_feature | Extract features from NMF run results |
nmf_extract_group | Extract groups (sample clustering) from NMF run results |
nmf_plot | Summary plot for NMF result |
nmf_select_best_k | Select the best k from multiple consensus NMF run |
nmf_silhouette_plot | Silhouette plot for NMF run |
nmf_summary | Get NMF run summary stats |
norm_factors | Calculate DESeq normalization factor |
parse_tsne_res | Extract and parse tsne results |
pcaplot | simple PCA plot |
plot_gene_expression | Plot expression for each gene |
plot_modules | Loop through each of the modules and connect the adjacent... |
plot_tsne | Plot t-SNE results |
predict_from_centroid | Predict group assignment from centroids |
preprocessNetCon | Preprocess the connecitivty matrix based on mean connectivity... |
reorderfun | Reorder dendrogram based on mean expression for RNA-Seq |
rmv_constant_0 | Remove genes that with too many constant 0 expression across... |
run_ClaNC | ClaNC run |
run_CoExpression | Preprocess the connecitivty matrix based on mean connectivity... |
run_CV | Run Cross-Validation |
run_DESeq2 | Run DEseq2 |
run_icash | Wrapper function to run the icahs Shiny App |
run_tsne | Use multi-core to run t-SNE |
sake | sake. |
scale_data | Scale data base on specify metrics |
screenshot_plotly | Screen shot of plotly object |
select_n_pct | Select top n percentage of data |
select_top_n | Select top number from a vector |
simpleCap | Convert letter to capitalization |
summarize_module2 | Identify the the edge of the modules (blocks) within the net... |
top_genes | Select top n genes |
Usoskin | Data from Usoskin et al |
vst | Use vst (fast) in DESeq2 |
weighted.silhouette | calculate weighted silhouette_width as threshold for running... |
wgcna_ext_hubgenes | Extract hub genes in each module by using WGCNA |
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