Closed PauBadiaM closed 2 years ago
Some method's names have been changed to make them easier to identify:
pscira
wsum
mean
wmean
scira
ulm
The column name for tf in the output tibbles has been changed to source.
tf
source
Updated documentation for all methods.
Updated vignette and README.
decouple function now accepts order mismatch between the list of methods and the list of methods's arguments.
decouple
Moved benchmark branch to a separate repository as its own package: https://github.com/saezlab/decoupleRBench
New methods added:
fgsea
AUCell
udt
mdt
mlm
New decoupleR manuscript repository: https://github.com/saezlab/decoupleR_manuscript
decoupleR
New consensus score based on RobustRankAggreg::aggregateRanks() added when running decouple with multiple methods.
consensus
RobustRankAggreg::aggregateRanks()
Methods based on permutations or statistical tests now return also a p-value for the obtained score (fgsea, mlm, ora, ulm, viper, wmean and wsum).
ora
viper
New error added when network edges are duplicated.
New error added when the input matrix contains NAs or Infs.
decoupleR 2.0.0
Changes
Some method's names have been changed to make them easier to identify:
pscira
now is called Weighted Sum (wsum
).mean
now is called Weighted Mean (wmean
).scira
now is called Univariate Linear Model (ulm
).The column name for
tf
in the output tibbles has been changed tosource
.Updated documentation for all methods.
Updated vignette and README.
decouple
function now accepts order mismatch between the list of methods and the list of methods's arguments.Moved benchmark branch to a separate repository as its own package: https://github.com/saezlab/decoupleRBench
New features
New methods added:
fgsea
).AUCell
.udt
).mdt
).mlm
).New
decoupleR
manuscript repository: https://github.com/saezlab/decoupleR_manuscriptNew
consensus
score based onRobustRankAggreg::aggregateRanks()
added when runningdecouple
with multiple methods.Methods based on permutations or statistical tests now return also a p-value for the obtained score (
fgsea
,mlm
,ora
,ulm
,viper
,wmean
andwsum
).New error added when network edges are duplicated.
New error added when the input matrix contains NAs or Infs.