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tothpetroczylab
DeMAG
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v1.0
DeMAG
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authors
Anna Hadarovich
hadarovi
Ksenia K
kuznetso
landerer
landerer
luppino
luppino
schereme
schereme
sghosh
sghosh
tothpet
tothpet
zzhu
zzhu
8 authors
May 10, 2023
Update README.md
· 83741f92
luppino
authored
1 year ago
83741f92
Feb 27, 2023
training set used to train DeMAG model (with exception of HGMD variants)
· 01e6bf20
luppino
authored
1 year ago
01e6bf20
Dec 15, 2022
edits
· ea473043
luppino
authored
2 years ago
ea473043
edits
· badccae2
luppino
authored
2 years ago
badccae2
modified idd
· 541a4746
luppino
authored
2 years ago
541a4746
Dec 13, 2022
all predictions for 257 ClinVar genes
· 5cb78c03
luppino
authored
2 years ago
5cb78c03
Dec 06, 2022
DeMAG predictions for all missense substitutions for acmg59 genes
· b1b00b9d
luppino
authored
2 years ago
b1b00b9d
Nov 25, 2022
testing set of estonian variants
· 75ae74a8
luppino
authored
2 years ago
75ae74a8
Nov 22, 2022
updated tutorial on DeMAG generalizability
· d73b9be5
luppino
authored
2 years ago
d73b9be5
Nov 17, 2022
added some function
· bbebc3a7
luppino
authored
2 years ago
bbebc3a7
radius of gyration for AlphaFold2 ACMG SF v2.0 3D models
· d95cddd4
luppino
authored
2 years ago
d95cddd4
test on training performance against ClinPred and VARITY
· 9a7011c8
luppino
authored
2 years ago
9a7011c8
changed filter on angstrom distance between c-alpha atoms
· 0c68b227
luppino
authored
2 years ago
0c68b227
Nov 10, 2022
github output
· 0bb8ad6c
luppino
authored
2 years ago
0bb8ad6c
changed output format to guthub output document.
· 89f5ac32
luppino
authored
2 years ago
89f5ac32
HTML report of Rmd file.
· 0da78002
luppino
authored
2 years ago
0da78002
R Rmd file to run predictions and evaluate performance on 334 genes.
· da71bb8a
luppino
authored
2 years ago
da71bb8a
AlphaFold pLDDT scores for the 334 genes.
· 2ae5c606
luppino
authored
2 years ago
2ae5c606
Partners score for the 334 genes.
· b7e9e503
luppino
authored
2 years ago
b7e9e503
IUPred2A disorder scores for the 334 genes.
· ee5551cc
luppino
authored
2 years ago
ee5551cc
precomputed EVmutation scores for the 334 genes.
· 0ba4faad
luppino
authored
2 years ago
0ba4faad
Description of the 334 genes selected for evaluation.
· c90cb979
luppino
authored
2 years ago
c90cb979
ClinVar high-quality pathogenic missense variants
· 4e735d0a
luppino
authored
2 years ago
4e735d0a
fixed typo
· 6dd12493
luppino
authored
2 years ago
6dd12493
Jun 16, 2022
Update README.md
· 4d4389fa
luppino
authored
2 years ago
v1.0
4d4389fa
partners score for co-evolving and spatially close residues
· d50047b4
luppino
authored
2 years ago
d50047b4
partners score for spatially close residues in the 3D space of the protein
· 33951c73
luppino
authored
2 years ago
33951c73
partners score for co-evolving residues in the linear space of the protein
· be291d29
luppino
authored
2 years ago
be291d29
Update README.md
· d4acbb65
luppino
authored
2 years ago
d4acbb65
training gbm model for DeMAG
· 0100dc31
luppino
authored
2 years ago
0100dc31
DeMAG model trained without ClinVar testing set as R object
· 6dcafbf1
luppino
authored
2 years ago
6dcafbf1
DeMAG model as R object
· 838ca97d
luppino
authored
2 years ago
838ca97d
Jun 15, 2022
update text
· 2bd4817b
luppino
authored
2 years ago
2bd4817b
benchmark DeMAG performance on functional testing set
· 190bd4bc
luppino
authored
2 years ago
190bd4bc
benchmark DeMAG performance on clinvar testing set
· 5b233010
luppino
authored
2 years ago
5b233010
functional testing set from DMS data for 4 acmg sf genes
· 720f4bd1
luppino
authored
2 years ago
720f4bd1
clinical testing set from clinvar (only variants submitted after year 2017)
· d5e9fa86
luppino
authored
2 years ago
d5e9fa86
partners score for acmg sf genes used for demag without clinvar testing set
· 45ce4272
luppino
authored
2 years ago
45ce4272
partners score for acmg sf genes
· 73f0b40f
luppino
authored
2 years ago
73f0b40f
alphafold plddt for acmg sf genes
· 58d04277
luppino
authored
2 years ago
58d04277