Package index

All functions

BUM_dens_sign()

Beta Uniform Mixture density function

DESeq2_test()

DESeq2_test: differential expression analysis of RNASeq data using DESeq2

Limma_v_test()

Limma_v_test: differential expression analysis of RNASeq data using Limma + Voom

dissimilarity_correlation()

dissimilarity_correlation

edgeR_test()

edgeR_test: differential expression analysis of RNASeq data using edgeR

generate_permutation_dist()

Generate CIBRA impact score permutation distribution

permutation_test()

CIBRA impact score permutation test

randomization()

Randomized CIBRA signal measure calculation

run_CIBRA()

Computationally identify biologically relevant alterations

scale_distance()

scale_distance calculates the similarity scores Uses the diffential expression states to calculate the similarity and anti-similarity scores.

score_assignment()

Assign score to the genes depending on in which box they lay in the volcano plot

signal_measures()

calculate the CIBRA signal measures Calculate the significant area and proportion from a p-value distribution

similarity_measures()

CIBRA similarity score

volcano_de_state_plot()

Volcano differential expression state plot