KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Biological samples | ||
|
| ||
| PCAWG project (core WGS dataset) Somatic Mutations and Mutational Catalogs from PCAWG Project | Alexandrov et al.4 | https://www.synapse.org/#!Synapse:syn11804058 https://www.synapse.org/#!Synapse:syn11804040 |
| PCAWG project (additional WGS dataset) VCF like sample files and SBS signatures in samples | Alexandrov et al.4 |
https://www.synapse.org/#!Synapse:syn11801872
https://www.synapse.org/#!Synapse:syn11801496 |
| MUTOGRAPHS project | Moody et al.7 | https://doi.org/10.6084/m9.figshare.22744733 |
|
| ||
| Deposited data | ||
|
| ||
| Topography of Mutational Signatures in Human Cancer | This paper | COSMIC Signatures v3.3https://cancer.sanger.ac.uk/signatures |
|
| ||
| Software and algorithms | ||
|
| ||
| SigProfilerMatrixGenerator (v1.1.31) | Bergstrom et al.65 | https://github.com/AlexandrovLab/SigProfilerMatrixGenerator |
| SigProfilerSimulator (v1.1.2) | Bergstrom et al.66 | https://github.com/AlexandrovLab/SigProfilerSimulator |
| SigProfilerExtractor (v1.1.0) | Islam et al.5 | https://github.com/AlexandrovLab/SigProfilerExtractor |
| SigProfilerClusters (v1.0.11) | Bergstrom et al.63 | https://github.com/AlexandrovLab/SigProfilerClusters |
| SigProfilerTopography (v1.0.70) | This paper | https://github.com/AlexandrovLab/SigProfilerTopography |
| Cancer-type specific and across all cancer-types combined topography analysis | This paper | https://github.com/AlexandrovLab/SigProfilerTopographyCombined |
| bigWigToWig tool (v446 April 2023) | Kent et al.67 | http://hgdownload.cse.ucsc.edu/admin/exe/ |
| liftOver tool (v446 April 2023) | Kent et al.67 | http://hgdownload.cse.ucsc.edu/admin/exe/ |
| Python (v3.7.0) | Python Software Foundation | https://www.python.org/ |
| Python package: pandas (v1.1.5) | McKinney68 | https://pandas.pydata.org |
| Python package: NumPy (v1.20.1) | Harris et al.69 | https://numpy.org |
| Python package: matplotlib (v3.4.2) | Hunter70 | https://matplotlib.org |
| Python package: SciPy (v1.6.3) | Virtanen et al.71 | https://scipy.org |
| Python package: statsmodels (v0.12.2) | Seabold and Perktold72 | https://www.statsmodels.org |
|
| ||
| Other | ||
|
| ||
| Transcription factors (TF) binding sites datasets (TF ChIP-seq assays) | ENCODE Project |
https://www.encodeproject.org/ Exact file name(s) for each utilized dataset is available as part of Table S1 |
| Histone modifications sites datasets (Histone ChIP-seq assays) | ENCODE Project |
https://www.encodeproject.org/ Exact file name(s) for each utilized dataset is available as part of Table S1 |
| Nucleosome occupancy datasets (MNase-seq assays) | ENCODE Project |
https://www.encodeproject.org/ Exact file name(s) for each utilized dataset is available as part of Table S1 |
| Replication timing datasets (Repli-seq assays) | ENCODE Project |
https://www.encodeproject.org/ Exact file name(s) for each utilized dataset is available as part of Table S1 |