From: ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
Method | Ref. | Input | Output | Clinical data? | Availability | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Prop. | Expr. | Individual | Cancer | Normal blood | Other | R | CellMix | MATLAB | Other | |||
profile | ||||||||||||
ISOpure (Quon) | [33] | tumour & unmatched normal | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||||
DeMix (Ahn) | [32] | tumour & unmatched normal | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||||||
Clarke | [30] | paired mixed & pure profiles | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||||
Gosink | [31] | mixed profiles and known profile of one constituent | \(\checkmark \) | \(\checkmark \) | ||||||||
DeconRNASeq (Gong) | [18] | profiles of constituents | \(\checkmark \) | \(\checkmark \) | ||||||||
Gong | [19] | cell-type specific gene signatures | \(\checkmark \) | \(\checkmark \) | ||||||||
Abbas | [20] | cell-type specific gene signatures | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||||
Wang M. | [21] | cell-type specific gene signatures | \(\checkmark \) | |||||||||
Lu | [22] | cell-type specific gene signatures | \(\checkmark \) | * | ||||||||
PERT (Qiao) | [46] | reference profiles of constituents | \(\checkmark \) | † | † | \(\checkmark \) | \(\checkmark \) | |||||
ESTIMATE (Yoshihara) | [47] | prior data used to derive cell-type specific gene signatures | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||||
DSection (Erkkilä) | [12] | prior knowledge of proportions | † | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||||||
csSAM (Shen-Orr) | [13] | proportions of constituents | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||||||
Bar-Joseph | [14] | proportions of consitutents, one expression profile | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||||
Ghosh | [16] | proportions, tumour & unmatched normal | \(\checkmark \) | \(\checkmark \) | * | |||||||
Stuart | [17] | proportions of constitutents | \(\checkmark \) | \(\checkmark \) | ||||||||
TEMT (Li) | [48] | prior knowledge of proportions, paired mixed-pure profiles | \(\checkmark \) | \(\checkmark \) | ||||||||
DSA (Zhong) | [23] | cell markers | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||
ssNMF (Gaujoux) | [25] | cell markers | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||||||
PSEA (Kuhn) | [24] | cell markers | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||||||
deconf (Repsilber) | [26] | cell markers | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||
Tolliver | [49] | tumour profile, number of constituents | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||||
Roy | [50] | prior estimate of number of constituents | \(\checkmark \) | \(\checkmark \) | ||||||||
Lähdesmäki | [15] | mixed expression profiles | † | \(\checkmark \) | ||||||||
Venet | [27] | mixed expression profiles, number of constituents | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |||||||
UNDO (Wang N.) | [51] | mixed expression profiles | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) |