Module methods 

This module contains Rust-based methods of various common bioinformatics methods, accelerated and optimised were possible via multi-threading and data structures with good cache locality

Modules

cis_target

Implementation of the RCisTarget algorithm from Aibar, et al., Nat Methods, 2018.

coremo

Implementation of the CoReMo workflow from François, et al., Nat Commun, 2024

dgrdl

Implementation of the dual graph regularised sparse dictionary learning based on the work of Pan, et al., Cell Syst, 2022

diffcor

Implementation of differential correlation method based on the Fisher method

graph_diffusions

Implementation of the tied diffusion method from Paull, et al., Bioinformatics, 2013

ica

Implementation of independent component analysis, based on the fastICA from Hyvrinen and Oja, Neural Comput., 1997

lda

Latent Dirichlet allocation by variational Bayes, for sparse count and binary matrices.

multi_cca

Sparse multiple canonical correlation analysis by penalised matrix decomposition.

nmf_bulk

Wrapper functions to run NMF on (likely) bulkRNAseq experiments of shape samples x features

nmf_hals

Implementation of NMF, dense and sparse paths. This version implements HALS with random or NNDSVD initialisation.

rbh

Implementations of the reciprocal best hit (RBH) methods for intersections or correlations, based on the works of Cantini, et al., Bioinformatics, 2019

snf

Similarity network fusion implementation based on Wang, et al., Nat Methods, 2014