KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Software and algorithms
BayesDeBulk	Petralia et al.7	https://github.com/wanglab-mssm/bayesdebulk
ESTIMATE	Yoshihara et al.83	https://bioinformatics.mdanderson.org/estimate/rpackage.html
TSNet	Petralia et al.84	https://github.com/petraf01/TSNet
GSVA	Hä nzelmann et al.85	https://bioconductor.org/packages/release/bioc/html/GSVA.html
ConsensusClusterPlus	Wilkerson et al.86	https://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html
ImmuneSubtypeClassifier	Gibbs et al. 87	https://github.com/CRI-iAtlas/ImmuneSubtypeClassifier
Enrichr	Chen et al.88	https://maayanlab.cloud/Enrichr/
Pamr	Tibshirani et al. 89	https://cran.r-project.org/web/packages/pamr/index.html
Glmnet	Friedman et al.90	http://r.meteo.uni.wroc.pl/web/packages/glmnet/glmnet.pdf
ClusterProfiler	Yu et al.91	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Msigdbr	Liberzon et al.92	https://igordot.github.io/msigdbr/
Impute	Hastie et al.93	https://www.bioconductor.org/packages//2.12/bioc/html/impute.html
MatrixeQTL	Shabalin et al.94	https://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/
KEA3	Kuleshov et al.9	https://maayanlab.cloud/kea3/
ChEA3	Keenan et al.62	https://maayanlab.cloud/chea3/
Panoptes - TensorFlow (v2)	Wang et al.11	https://github.com/Wenke-Liu/panoptes
Panoptes – TensorFlow (v1)	Hong et al.10	https://github.com/rhong3/CPTAC-UCEC
Tensorflow	Abadi et al.95	https://www.tensorflow.org
Inception	Szegedy et al.96	https://github.com/google/inception
InceptionResNet	Szegedy et al.96	https://github.com/tensorflow/models/tree/master/research/slim/nets
Keras	Chollet, F., and others (2015).	https://keras.io
DACT	Liu et.al.97	https://github.com/zhonghualiu/DACT
SigComLincs	Evangelista et al.63	https://maayanlab.cloud/sigcom-lincs/
DreamAI	Ma et al.98	https://github.com/WangLab-MSSM/DreamAI
The Kinase Library	Johnson et al.8	https://kinase-library.phosphosite.org/