Man pages for naikai/sake
Single-cell RNA-Seq Analysis and Klustering Evaluation

affy_probe_to_gene_symboluse hgu133a.db or hgu133plus2.db to convert from affymetrix...
assign_label_cexAdjust label cex based on its number
cal_entropycalculate entroyp
centroid_classifyClassify samples based on the feed in centroids
clean_iterNMFExtract, cleanup, and merge iter_NMF results
clust_by_hierClustering by hierarchical
compare_groupCompare two groups assignment results
compare_groups_statsCalculate statistics comparing two clustering results
comp_module_genelistCompute module gene list
connect_gap_modulesLoop through each of the modules and connect the adjacent...
corModuleUISample correlation plot
cor_mtestload predefined gene list files for heatmap
create.brewer.colorCreate brewer color
create_centroidCreate centroid based on the grouping info
create.manual.colorManually specify coloring for provided groups
def_net_module2Identify the the edge of the modules (blocks) within the net...
def_net_modulesIdentify the the edge of the modules (blocks) within the net...
deseq_normNormalize data through DESeq size factor
detect_genecnt_IDAutomatically convert genecnt into Entrez ID
detect_genecnt_platformCheck rownames from data and auto detect which platform it is...
ext_gene_functionExtract ensembl_id using gene symbol
extract_data_by_madExtract data by MAD value
extract_data_by_mathExtract data by 'math' operation
gene_convert_human_to_mouseUse biomaRT to convert human gene to mouse gene
gene_convert_mouse_to_humanuse biomaRT to convert mouse gene to human gene
get_ClaNC_groupGet ClaNA Group info
heatmap.3Published version of heatmap.3, with more options
helloHello, World!
is.wholeCheck whether it is a integer whole value
iter_nmfRun iterative NMF for K=2 until it cannot no longer separate...
load_genelistload predefined gene list files for heatmap
load_genesetload predefined gene set files for GSEA
module_finderIdentify the modules in Data within co-expression network
multiplotMultiple plot function
mutual_info_from_confmatrixCalculate Mutual information from confusion matrix
mutual_info_from_vectorcalculate Mutual information from two vector
myboxplotCustom version of boxplot
myd3HeatmapCustom version of d3heatmap
myfread.tableUse data.table for faster read.table
myHeatmap.3A Cat Function
myNMFFunction to run NMF with different options
my.write.matrixOwn version of writing matrix output
name_to_colorConvert name to color
NetConnectivityIdentify the informative genes in Data with top high...
nmf_estim_plotGenerate individual plot for estimating K
nmf_extract_featureExtract features from NMF run results
nmf_extract_groupExtract groups (sample clustering) from NMF run results
nmf_plotSummary plot for NMF result
nmf_select_best_kSelect the best k from multiple consensus NMF run
nmf_silhouette_plotSilhouette plot for NMF run
nmf_summaryGet NMF run summary stats
norm_factorsCalculate DESeq normalization factor
parse_tsne_resExtract and parse tsne results
pcaplotsimple PCA plot
plot_gene_expressionPlot expression for each gene
plot_modulesLoop through each of the modules and connect the adjacent...
plot_tsnePlot t-SNE results
predict_from_centroidPredict group assignment from centroids
preprocessNetConPreprocess the connecitivty matrix based on mean connectivity...
reorderfunReorder dendrogram based on mean expression for RNA-Seq
rmv_constant_0Remove genes that with too many constant 0 expression across...
RPMTransform the countdata into Reads per million reads
run_ClaNCClaNC run
run_CoExpressionPreprocess the connecitivty matrix based on mean connectivity...
run_CVRun Cross-Validation
run_DESeq2Run DEseq2
run_icashWrapper function to run the icahs Shiny App
run_tsneUse multi-core to run t-SNE
sakesake.
scale_dataScale data base on specify metrics
screenshot_plotlyScreen shot of plotly object
select_n_pctSelect top n percentage of data
select_top_nSelect top number from a vector
simpleCapConvert letter to capitalization
summarize_module2Identify the the edge of the modules (blocks) within the net...
top_genesSelect top n genes
UQTransform the countdata by upper quantile value from each...
UsoskinData from Usoskin et al
vstUse vst (fast) in DESeq2
weighted.silhouettecalculate weighted silhouette_width as threshold for running...
wgcna_ext_hubgenesExtract hub genes in each module by using WGCNA
naikai/sake documentation built on April 13, 2018, 8:44 p.m.