| Deposited data |
|
| PCAWG data |
ICGC/PCAWG |
https://dcc.icgc.org/pcawg |
|
| Software and algorithms |
|
| Consensus-bp |
This paper |
https://github.com/morrislab/consensus-bp |
| icgc_consensus_copynumber |
This paper |
https://github.com/sdentro/icgc_consensus_copynumber |
| icgc_consensus_purity |
This paper |
https://github.com/sdentro/icgc_consensus_purity |
| CICC |
This paper |
https://github.com/galder-max/CICC |
| CSR |
This paper |
https://github.com/wwylab/CSR |
| weme |
This paper |
https://github.com/morrislab/weme |
| MutationTimeR |
Gerstung et al., 2020 |
https://github.com/gerstung-lab/MutationTimeR |
| icgc_consensus_clustering_assignment |
This paper |
https://github.com/sdentro/icgc_consensus_clustering_assignment |
| SimClone1000 |
This paper |
https://github.com/galder-max/SimClone1000 |
| SpoilSport |
This paper |
https://github.com/morrislab/SpoilSport |
| ABSOLUTE |
Carter et al., 2012 |
https://software.broadinstitute.org/cancer/cga/absolute |
| Aceseq |
Kleinheinz et al., 2017 |
https://github.com/DKFZ-ODCF/ACEseqWorkflow |
| Battenberg |
Dentro et al., 2017; Nik-Zainal et al., 2012
|
https://github.com/Wedge-lab/battenberg |
| CloneHD |
Fischer et al., 2014 |
https://github.com/andrej-fischer/cloneHD
https://github.com/ivazquez/cloneHD-PCAWG
|
| JabBa |
Hadi et al., 2019 |
https://github.com/mskilab/JaBbA |
| Sclust |
Cun et al., 2018 |
http://www.uni-koeln.de/med-fak/sclust/Sclust.tgz |
| BayClone |
Sengupta et al., 2015 |
https://github.com/compgenome365/bayclonec/tree/compgenome365-pcawg |
| Ccube |
Yuan et al., 2018 |
https://github.com/keyuan/ccube |
| CliP |
This paper |
https://github.com/wwylab/CliP |
| CTPsingle |
Donmez et al., 2017 |
https://github.com/nlgndnmz/CTPsingle |
| DPClust |
Nik-Zainal et al., 2012 |
https://github.com/Wedge-lab/dpclust |
| PhylogicNDT |
Leshchiner et al., 2019 |
https://github.com/broadinstitute/PhylogicNDT |
| PhyloWGS |
Deshwar et al., 2015 |
https://github.com/morrislab/phylowgs |
| PyClone |
Roth et al., 2014 |
https://github.com/Roth-Lab/pyclone |
| Sclust |
Cun et al., 2018 |
http://www.uni-koeln.de/med-fak/sclust/Sclust.tgz |
| SVclone |
Cmero et al., 2020 |
https://github.com/mcmero/SVclone |
| RandomClone |
This paper |
https://github.com/sdentro/randomclone |
| TrackSig |
Rubanova et al., 2020 |
https://github.com/morrislab/TrackSig |
