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mskilab-org
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JaBbA
MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
MIT License
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save purity ploidy values to a table
#55
ShaiberAlon
closed
2 years ago
0
Bigwig patch
#54
zining01
closed
2 years ago
0
Auto epgap
#53
zining01
closed
3 years ago
1
filter.loose failing when flanking node contains just 2 coverage bins
#52
ShaiberAlon
closed
3 years ago
1
fix max.na bins and ab.edges/ab.force indexing bug
#51
zining01
closed
3 years ago
0
Update README.md
#50
xtYao
closed
3 years ago
1
remove NA's when checking junction tier
#49
zining01
closed
3 years ago
1
Ism conflict
#48
zining01
closed
3 years ago
1
Junction balance
#47
zining01
closed
3 years ago
1
fix hets.txt example and fix test_JaBbA accordingly
#46
ShaiberAlon
closed
3 years ago
1
About input hets files
#45
icelu
closed
3 years ago
2
add junction forcing for tier 1 junctions
#44
zining01
closed
3 years ago
1
install_bug
#43
zining01
closed
3 years ago
1
lpv2
#42
zining01
closed
3 years ago
1
incorporate Julie new function filter.loose from loosends package com…
#41
xtYao
closed
3 years ago
0
Dev
#40
xtYao
closed
3 years ago
1
Error in smooth.spline(fdat$lag, fdat$ac, spar = spar) : 'tol' must be strictly positive and finite
#39
FreyaVan
closed
3 years ago
0
Failed install JaBbA package
#38
Kingsman-Key
closed
3 years ago
2
Generate coverage txt file using GRIDSS-PURPLE-LINX
#37
alhafidzhamdan
closed
3 years ago
4
revert the handling of BEDPE header
#36
xtYao
closed
3 years ago
0
Dev
#35
xtYao
closed
3 years ago
0
fixing the het.file fail
#34
xtYao
closed
3 years ago
0
Difficulty installing the package(s)
#33
alhafidzhamdan
closed
3 years ago
12
Error running the test case
#32
wkljohn
closed
3 years ago
1
Resolve all NAMESPACE conflicts
#31
xtYao
closed
3 years ago
0
big commit before 1.0 release
#30
xtYao
closed
3 years ago
0
Using --nseg with sequenza purity/ploidy estimation
#29
willhooper
closed
3 years ago
1
Problem size limits exceeded
#28
mjko1210
closed
3 years ago
6
definition of coverage
#27
mjko1210
closed
3 years ago
2
'Rcplex2.o' failed
#26
mjko1210
closed
4 years ago
2
A couple files not written to output directory
#25
willhooper
closed
3 years ago
2
installation fails with "Skipping 1 packages not available: bamUtils"
#24
funnell
closed
3 years ago
3
JaBbA.R contains calls to info from VariantAnnotation without using package name
#23
pwaltman
closed
3 years ago
0
License
#22
walaj
closed
3 years ago
1
fragCounter automatically strips out 'chr' from the chromosome names in the final cov.rds output
#21
pwaltman
closed
5 years ago
2
in ramip_stub function, call 'es = data.table(which(adj!=0, arr.ind=T))' on line 1835 uses base which function, rather than Matrix::which
#20
pwaltman
closed
5 years ago
2
JaBbA crashes when DNAcopy::segment returns reverse strand segments
#19
pwaltman
closed
11 months ago
3
jba is not passing the coverage and junctions arguments to the JaBbA correctly
#18
pwaltman
closed
5 years ago
7
new encrypted link to dep
#17
xtYao
closed
5 years ago
0
`ppgrid` fails when purity is set but not ploidy
#16
xtYao
opened
5 years ago
0
"karyograph.rds.ppgrid.pdf" is NOT readable
#15
chunyangbao
closed
3 years ago
1
Fixed sequenza being deactivated in karyograph_stub due to typo
#14
chunyangbao
closed
5 years ago
0
Remove redundant dependencies: copynumber
#13
xtYao
closed
3 years ago
1
Make the C functions compilation compatible with MacOS
#12
xtYao
closed
11 months ago
1
add warning when the user's optimizer is not fully functional
#11
xtYao
closed
3 years ago
2
L1.opt
#10
xtYao
closed
6 years ago
0
merging New.loose
#9
xtYao
closed
6 years ago
0
Loose end penalty new mode: penalize number of loose ends regardless of copy number
#8
xtYao
closed
6 years ago
1
Xt debug
#7
xtYao
closed
6 years ago
1
Many robustness improvements
#6
xtYao
closed
6 years ago
0
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