Some tools that you can use (non-exhaustive)

Methylome

Unsupervised

RefFreeEWAS Houseman et al, 2016, BMC bioinformatics, PMID 27358049 [NMF]

MeDeCom Lutsik et al, 2017, Genome Biology, PMID 28340624 [NMF]

Semi-supervised

EDec Onuchic et al, 2017, Cell reports, PMID 27851969 [NMF]

Supervised

EpiDISH Teschendorff et al, 2017, Epigenomics, PMID 28517979 [SVR, RPC or CP]

Toolbox R package

medepir Decamps et al, 2019, In revision in BMC Bioinformatics, [pipeline for RefFree methods]

Transcriptome

Unsupervised

DeconICA Czerwinska et al. [ICA]

Decoder Peng et al 2019, Nature communications. [NMF + NNLS]

deconf Repsilber et al., 2010, BMC bioinformatics. [Random Forest + NNLS]

Semi-supervised

Deblender Dimitrakopoulou et al 2018, Bioinformatics. [NMF](MATLAB)

WISP Blum et al 2019, Nature communications. [NNLS]

DSA Zhong et al., 2013, BMC bioinformatics. [NNLS]

Supervised

DeconvSeq Du et al 2019 Bioinformatics. [GLM]

LRCDE Glass and Dozmorov, 2016, BMC bioinformatics. [LM]

MMAD Liebner et al 2014, Bioinformatics. [Maximum likelihood/ Conjugate gradient](MATLAB)

DeconRNASeq Gong and Szustakowski, 2013, Bioinformatics. [NNLS]

MuSic Wang et al 2019, Nature communications. [NNLS]

Toolbox R package

CellMix Gaujoux and Seoighe, 2013, Bioinformatics. [including DSA and deconf, NMF]