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hartwigmedical
/
hmftools
Various algorithms for analysing genomics data
GNU General Public License v3.0
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ORANGE (v2.5.0) could not find features plots from CUPPA (v1.8)
#428
YingYa
closed
9 months ago
1
ORANGE (v2.5.0) failed to load LINX (v1.23.6) plots
#427
YingYa
closed
11 months ago
1
Bump scipy from 1.5.4 to 1.10.0 in /cuppa/src/main/resources/cuppa-chart
#426
dependabot[bot]
closed
7 months ago
1
DEV-3374 configure cloud build
#425
KasperWolsink99
closed
10 months ago
1
Dev 3451
#424
charlesshale
closed
1 year ago
0
DEV-3374 cloudbuild WIP
#423
KasperWolsink99
closed
1 year ago
0
Orange - problem with flagstat file
#422
kstawiski
closed
1 year ago
2
gnomAD annotation - PAVE (1.4.2)
#421
anaduba
closed
1 year ago
2
LILAC MHC Class II support?
#420
mflevine
closed
1 year ago
1
Just quick question about the purity adjusted value
#419
nan5895
closed
1 year ago
6
[ERROR] cannot find sequence index for chromosome 6 in bam header -- hg19
#418
raerose01
closed
1 year ago
1
ACTIN-170 Persist/read the config with the orange record
#417
pauldwolfe
closed
1 year ago
1
Change "gender" to "sex" in PURPLE outputs
#416
nalcala
closed
1 year ago
1
Lilac on WES data
#415
AAAapollo
closed
1 year ago
5
Bump guava from 31.0.1-jre to 32.0.0-jre
#414
dependabot[bot]
closed
7 months ago
1
DEV-3317 include non-canonical transcripts in orange
#413
KasperWolsink99
closed
1 year ago
0
ACTIN-151: Fix expression selection bug for unknown cohort
#412
jbartletthmf
closed
1 year ago
0
PURPLE: short segments with CN=2.00 and method=UNKNOWN
#411
e-sollier
closed
1 year ago
2
ACTIN-117 Allow for deserialization from any Reader
#410
pauldwolfe
closed
1 year ago
0
ACTIN-141: Include individual CUPPA classifier data in ORANGE output
#409
jbartletthmf
closed
1 year ago
0
ACTIN-144: Maintain linx clusters after ORANGE germline conversion
#408
jbartletthmf
closed
1 year ago
0
cobalt error on long read data
#407
jiadong324
closed
11 months ago
12
Is it possible to have PURPLE report any germline missense variants in a selected gene(s)?
#406
toddajohnson
closed
9 months ago
2
PURPLE ERROR
#405
YuP9934
closed
1 year ago
4
Orange for panel output
#404
davidvanzessen
closed
1 year ago
1
DEV-3251 Missed expected clonal coverage
#403
pauldwolfe
closed
1 year ago
0
DEV-3251 Fix the orange conversion for virus interpretation
#402
pauldwolfe
closed
1 year ago
0
SAGE exception: ... because "this.mRefContext" is null
#401
rod1Gene
closed
1 year ago
1
sage exception: "sequenceDictionary" is null
#400
rod1Gene
closed
1 year ago
2
SAGE problem: VCF header has duplicate sample names
#399
rod1Gene
closed
1 year ago
1
location of required input files
#398
rod1Gene
closed
1 year ago
2
realignment command for alt contigs
#397
rod1Gene
closed
1 year ago
4
Purity Interpretation
#396
DarioS
closed
1 year ago
1
LINX visualization for select regions
#395
lichennan123
closed
1 year ago
3
PURPLE_AF - how is it calculated?
#394
maia-munteanu
closed
1 year ago
5
Error executing R script in Amber
#393
msubirana
closed
1 year ago
13
[ERROR] cannot find sequence index for chromosome 6 in bam header
#392
rod1Gene
closed
1 year ago
2
Purple MACN in SV VCF
#391
jaesvi
closed
1 year ago
2
Regarding templated insertions in LINX
#390
jaesvi
closed
1 year ago
2
Quick question-- compatibility with long read data?
#389
jamesdalg
closed
1 year ago
1
GRIPSS 2.3.5 in -germline mode overwrites somatic GRIPSS VCF
#388
toddajohnson
closed
1 year ago
1
move orange datamodel assembly plugin dependency to orange pom
#387
mvanniekerkHartwig
closed
1 year ago
0
What are considered valid sample names for PURPLE?
#386
toddajohnson
closed
1 year ago
2
ACTIN-41: Add optional disclaimer to ORANGE
#385
jbartletthmf
closed
1 year ago
2
Fix orange datamodel artifact
#384
mvanniekerkHartwig
closed
1 year ago
0
ACTIN-33: Show CNs with 1 place after decimal in ORANGE
#383
jbartletthmf
closed
1 year ago
0
ACTIN-32: Improve formatting for undetermined HRD type
#382
jbartletthmf
closed
1 year ago
0
ACTIN-24: Use one instance of ReportResources to avoid duplicating fonts
#381
jbartletthmf
closed
1 year ago
0
Cannot find citation
#380
micoli98
closed
1 year ago
2
cider - Inappropriate call if not paired read
#379
3d7l
closed
3 months ago
3
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