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quinlan-lab
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pathoscore
pathoscore evaluates variant pathogenicity tools and scores.
MIT License
21
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8
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evaluation-set: saturation mutagenesis of PPARG
#70
brentp
opened
4 years ago
0
saturation mutagenesis of PTEN
#69
brentp
opened
4 years ago
0
Paper figures and scripts -- slight changes to pathoscore output for paper and enduser
#68
jimhavrilla
opened
5 years ago
0
fixes to metasvm, sift, polyphen (can simply not use cadd score precomputed)
#67
jimhavrilla
closed
5 years ago
1
permanently fix the J PDF problem, plus a color palette issue
#66
jimhavrilla
closed
5 years ago
0
try vega, fall back to 'tab' palettes
#65
brentp
closed
5 years ago
1
vega20, vega10 deprecated in pathoscore
#64
brentp
closed
5 years ago
1
clear axis for J score PDF
#63
jimhavrilla
closed
5 years ago
0
new gene sets and efficiency fixes to old gene formulae
#62
jimhavrilla
closed
6 years ago
6
new set of pathogenic variants
#61
brentp
opened
6 years ago
6
annotate for many fields per file
#60
jimhavrilla
closed
6 years ago
4
Primateai
#59
jimhavrilla
opened
6 years ago
2
make script fixes and checks
#58
jimhavrilla
closed
6 years ago
0
Missense Z constraint
#57
jimhavrilla
closed
6 years ago
4
RVIS
#56
jimhavrilla
closed
6 years ago
1
Exclusion for benigns
#55
jimhavrilla
closed
6 years ago
0
fix to freq step plot
#54
jimhavrilla
closed
6 years ago
3
pLI change, added in gene to file for more information
#53
jimhavrilla
closed
6 years ago
1
added precision recall to HTML, PDF, baseline calculations, legend
#52
jimhavrilla
closed
6 years ago
4
added MTR
#51
jimhavrilla
closed
6 years ago
0
fix to goi defaults, cleaned up some code
#50
jimhavrilla
closed
6 years ago
1
Two haploinsufficient gene sets
#49
jimhavrilla
closed
6 years ago
0
removed erroneous metrics, added precomputed metric scores for truth sets, MetaSVM
#48
jimhavrilla
closed
6 years ago
0
add ClinVar Benchmark sets
#47
jimhavrilla
closed
6 years ago
5
added phastcons
#46
jimhavrilla
closed
6 years ago
0
added haploinsufficient gene set and clinical utility description + default GOI
#45
jimhavrilla
closed
6 years ago
4
added CCR
#44
jimhavrilla
closed
6 years ago
0
add VVP
#43
jimhavrilla
closed
6 years ago
0
make.sh and readme.md for DANN scoring
#42
davemcg
closed
6 years ago
2
added DANN scoring
#41
davemcg
closed
6 years ago
4
added gnomAD and ExAC scripts, and an example for filtering on allele frequency
#40
jimhavrilla
closed
6 years ago
6
added clinical utility, moved and modified plotly_html generator script, and changed template to add table
#39
jimhavrilla
closed
6 years ago
3
add clinical utility table for a list of provided genes
#38
jimhavrilla
closed
6 years ago
5
inframe deletions, insertions, and splice vars added, and fixed bug for multiple CSQs
#37
jimhavrilla
closed
6 years ago
4
the link for the archive changed again, fixed, and updated to latest version in archive, added citation and text to README
#36
jimhavrilla
closed
6 years ago
0
added a lot of text and explanation to README, fixed gff lines in make.sh
#35
jimhavrilla
closed
6 years ago
0
added text to README, fixed fasta bug
#34
jimhavrilla
closed
6 years ago
4
improved samocha readme, and fixed fasta bug
#33
jimhavrilla
closed
6 years ago
0
fix to clinvar, pulling from one month old permanent archive link
#32
jimhavrilla
closed
7 years ago
0
ftp for clinvar true set has changed
#31
edgarjavi
closed
7 years ago
9
Fathmm no sorting
#30
qingl0331
closed
7 years ago
2
Newbranch
#29
qingl0331
closed
7 years ago
0
added aloft score
#28
jimhavrilla
closed
7 years ago
9
add phylop
#27
qingl0331
closed
7 years ago
15
add fathmm
#26
qingl0331
closed
7 years ago
5
added REVEL score set and README.md
#25
jimhavrilla
closed
7 years ago
0
text output
#24
brentp
closed
7 years ago
0
README and make.sh for M-CAP, added if statement for grabbing CADD set
#23
jimhavrilla
closed
7 years ago
1
README and make.sh for M-CAP, added if statement for grabbing CADD set
#22
jimhavrilla
closed
7 years ago
4
code for allowing no annotation with scores
#21
jimhavrilla
closed
7 years ago
7
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