Man pages for fossbert/binilib
Carlo's little helper

any2entrezConvert Symbols or Ensembl gene ids to Entrez Ids
any2symbolConvert Entrez or Ensembl gene ids to gene symbols
aREA_singleaREA for a single regulon
basic_rank_normBasic rank normalization of a gene expression matrix
basic_signaturebasic_signature
brks_heatmapCenter heatmap color gradient at zero
collapse_multiCollapsing many-to-one relationships for gene expression...
colorScalecolorScale
colVarcolVar
DEtransformVariance stabilization transformation for RNAseq data
extract_featuresExtract rows or columns from a matrix in order of interest
find_var_genesFinding the most variable features of a matrix
geneLengthsInformation on gene lengths. As derived from...
geneSets2regulonConvert regular (one-tailed) gene sets to regulons
gsea1-classThe gsea1 class
gsea1TThis function performs one-tailed Gene Set Enrichment...
gsea2-classThe gsea2 class
gsea2ESES for 2 tail GSEA (Lim et al., 2009) - two character vectors
gsea2ES_regulonES for 2 tail GSEA (Lim et al., 2009) - Regulons
gsea2TThis function performs GSEA of two gene sets for a given...
gsea_null-methodsGSEA null model
gsea_regulonThis function performs GSEA for the negative and positive...
gs_ovlpScore character vectors of genes and their overlap with...
homologyInfoHuman and Mouse Homology data Information on 16469 genes for...
homologyTableFull homology data as provided by Jax Information on a more...
kaboxplotPlot quantiles per column for a numeric matrix
lapply_pairlapply function to apply functions in a pair-wise manner...
legend_colAdd a custom color gradient to a base R plot
lrcorFor two matched matrices, compute correlation (Spearman)...
mouse2humanConvert mouse gene symbols or entrez ids to human...
myparQuick changes to the plotting environment
order_heatmapOrder the columns of a heatmap within the constraints of a...
p2zConvert p-values from a two tailed test to quantiles of the...
pick_probesFind best probe if there are multiple per gene
plot_fgseaResPlot one-tailed GSEA on one signature for multiple gene sets
plot.gsea1Plot results from a one-tailed GSEA
plot.gsea2Plot 2-tailed enrichment results
plot.gsea2regulonPlot 2-tailed enrichment results
plothmPlot heatmap
plot_OneGs_MultSigPlot ranks of a given gene set across several gene expression...
plot_OneReg_MultSigPlot two tails of one regulon on multiple signatures
purISTPurIST
randomize_esetrandomize_eset
randomize_regulonGenerate a randomized network
read_matrixTidyverse way to read in gene expression matrices
reexportsObjects exported from other packages
reg2tibbletransform a regulon object to a data frame / tibble
regulatorNamesInformation on 6068 regulatory genes used in the...
replace_missingsReplace missing values (typically in a vector or matrix)
rescale01Rescale a numeric vector to range between 0 and 1
res_msvipExtract msviper results
rowTstatCalculate row-wise Welch’s t-statistic
rowVarrowVar
specific_nFor a signature matrix containing conditions/comparisons in...
split_violinSplit violin plot
stouffer_zStouffer integration of Z scores
topN_matFor a numeric matrix containing samples or conditions in its...
tpmtpm
vpres2regulonExtract the top up and down regulated MR per sample
vpsig_limmaviperSignature and nullmodel using limma
write_matrixConvenience function for writing gene expression to file
fossbert/binilib documentation built on April 23, 2021, 10:31 p.m.