broadinstitute PhylogicNDT issues

broadinstitute / PhylogicNDT

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Is targeted sequencing data allowed?

#73 lincj1994 opened 1 month ago
1
Relative timing for subregion (chr3q13.33 instead of chr3q)

#72 oghzzang opened 3 months ago
0
Prior calculation performance for 1000+ mutations

#71 dlivitz opened 6 months ago
0
how to understand the result of com.tsv

#70 Elizabeth237 opened 11 months ago
1
input of SinglePatientTiming

#69 Elizabeth237 opened 11 months ago
2
tuple index out of range

#68 kangdong318 opened 1 year ago
0
About SinglePatientTiming demo

#67 RetGiraffe11235 opened 1 year ago
2
removed silent mutations from clonal trees

#66 eemartin42 opened 1 year ago
0
Retrieve the segment info of CNVs from the output

#65 lichennan123 opened 1 year ago
2
Protein_Change and Variant_Classification are None

#64 lincj1994 opened 1 year ago
2
Docker build fails

#63 emsisson opened 1 year ago
0
Is the CorrectBias module undefined?

#62 moshl opened 2 years ago
1
Bad clustering with combines 0 CCF and 1 CCF mutations

#61 SebastianHollizeck opened 2 years ago
0
Protein_change and Protein_Change are inconformity in different scripts.

#60 YingYa opened 2 years ago
0
More than one tree was generated in Phylogic Results

#59 angelacho0113 opened 2 years ago
0
Warnings with example data

#58 rpensch opened 2 years ago
1
Cluster CCF Trace, Cluster Colors, and Cell Pop bug fixes

#57 ConorMesser opened 2 years ago
0
What citation should be used for PhylogicNDT?

#56 bknisbac opened 2 years ago
0
SinglePatientTiming: get_arm_level_cn_events

#55 iS4i4S opened 3 years ago
5
`--order_by_timepoint` not working

#54 abenjak opened 3 years ago
0
Allele-specific copy number from PhylogicNDT or ABSOLUTE

#53 juberpatel opened 3 years ago
2
CCF of child cluster greater than parents

#52 nadia35 opened 3 years ago
1
cluster 1 with clust_ccf_mean equal 1 was the clonal cluster ?

#51 smm19900210 opened 3 years ago
1
"IndexError: list index out of range" in plot_1d_clusters

#50 SebastianHollizeck opened 4 years ago
2
specifying output folder for singularity

#49 SebastianHollizeck opened 4 years ago
3
Added support in GrowthKinetics for WBC records between samples

#48 jcha40 opened 4 years ago
0
buildtree not showing private mutations

#47 vicentepp opened 4 years ago
0
Running cluster step on hypermutated tumour mutations

#46 bkinnersley opened 4 years ago
0
PureCN implementation of ABSOLUTE as input for phylogicNDT

#45 naumenko-sa opened 4 years ago
1
ModuleNotFoundError: No module named 'Sample'

#44 vicentepp closed 4 years ago
1
Consolidated sif parser and command line parser & added seg_input_type as an argument

#43 jcha40 closed 4 years ago
0
A minor issue in SinglePatientTiming

#42 shwong-tw closed 2 years ago
0
MS Timing normalization & remove numba

#41 jcha40 closed 4 years ago
0
Log output destination configurable?

#40 csmith-pact opened 4 years ago
0
Min number of mutations in each cluster

#39 mksamur opened 4 years ago
1
[ref #10] fix missing argument for ccf histogram

#38 judithabk6 opened 4 years ago
0
docker permission denied each time

#37 xhy1219 opened 4 years ago
0
Reverted to drawing from low_coverage_mutations attribute in output

#36 jcha40 closed 4 years ago
0
Indels not added in after clustering

#35 aktewari opened 4 years ago
0
behavior parameter --impute

#34 shwong-tw closed 4 years ago
0
Implemented CCF calculation

#33 jcha40 closed 4 years ago
0
Fixed AttributeException in output

#32 jcha40 closed 4 years ago
0
Added check for unclustered mutations

#31 jcha40 closed 4 years ago
0
Put unclustered events in their own output file

#30 jcha40 closed 4 years ago
0
ABSOLUTE for CCF

#29 mkinnaman opened 4 years ago
7
CellPopulationEngine update

#28 jcha40 closed 4 years ago
0
Update GrowthKinetics

#27 jcha40 closed 4 years ago
0
Added timing report + bugfix in output generation

#26 jcha40 closed 4 years ago
0
Output + impute update

#25 jcha40 closed 4 years ago
0
Correct command in example notebook and update Dockerfile

#24 jcha40 closed 4 years ago
0