Code covered by the BSD License  

Highlights from
WTSI Mutational Signature Framework

image thumbnail

WTSI Mutational Signature Framework

by

 

23 Oct 2012 (Updated )

Framework for deciphering signatures of mutational processes from a set of mutational catalogues

code.zip
data/2012-Nik-ZainalEtAl-Cell/21_WTSI_BRCA_whole_genome_substitutions.mat
data/2013-AlexandrovEtAl-CellReports/100_WTSI_BRCA_whole_exome_substitutions.mat
data/2013-AlexandrovEtAl-CellReports/100_WTSI_BRCA_whole_exome_substitutions_strand_bias.mat
data/2013-AlexandrovEtAl-CellReports/21_WTSI_BRCA_whole_genome_substitutions.mat
data/2013-AlexandrovEtAl-CellReports/21_WTSI_BRCA_whole_genome_substitutions_dinucleotides_indels_kataegis.mat
data/2013-AlexandrovEtAl-CellReports/21_WTSI_BRCA_whole_genome_substitutions_pentanucleotides.mat
data/2013-AlexandrovEtAl-CellReports/21_WTSI_BRCA_whole_genome_substitutions_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/.DS_Store
data/2013-AlexandrovEtAl-Nature/exomes/ALL/ALL_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/ALL/ALL_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/ALL/ALL_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/AML/AML_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/AML/AML_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/AML/AML_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Bladder/Bladder_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Bladder/Bladder_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Bladder/Bladder_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Breast/Breast_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Breast/Breast_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Breast/Breast_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Cervix/Cervix_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Cervix/Cervix_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Cervix/Cervix_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/CLL/CLL_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/CLL/CLL_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/CLL/CLL_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Colorectum/Colorectum_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Colorectum/Colorectum_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Colorectum/Colorectum_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Esophageal/Esophageal_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Esophageal/Esophageal_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Esophageal/Esophageal_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Glioblastoma/Glioblastoma_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Glioblastoma/Glioblastoma_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Glioblastoma/Glioblastoma_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Glioma Low Grade/Glioma Low Grade_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Glioma Low Grade/Glioma Low Grade_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Glioma Low Grade/Glioma Low Grade_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Head and Neck/Head and Neck_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Head and Neck/Head and Neck_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Head and Neck/Head and Neck_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Chromophobe/Kidney Chromophobe_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Chromophobe/Kidney Chromophobe_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Chromophobe/Kidney Chromophobe_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Clear Cell/Kidney Clear Cell_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Clear Cell/Kidney Clear Cell_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Clear Cell/Kidney Clear Cell_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Papillary/Kidney Papillary_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Papillary/Kidney Papillary_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Kidney Papillary/Kidney Papillary_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Adeno/Lung Adeno_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Adeno/Lung Adeno_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Adeno/Lung Adeno_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Small Cell/Lung Small Cell_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Small Cell/Lung Small Cell_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Small Cell/Lung Small Cell_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Squamous/Lung Squamous_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Squamous/Lung Squamous_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lung Squamous/Lung Squamous_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lymphoma B-cell/Lymphoma B-cell_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lymphoma B-cell/Lymphoma B-cell_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Lymphoma B-cell/Lymphoma B-cell_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Melanoma/Melanoma_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Melanoma/Melanoma_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Melanoma/Melanoma_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Myeloma/Myeloma_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Myeloma/Myeloma_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Myeloma/Myeloma_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Neuroblastoma/Neuroblastoma_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Neuroblastoma/Neuroblastoma_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Neuroblastoma/Neuroblastoma_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Ovary/Ovary_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Ovary/Ovary_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Ovary/Ovary_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Pancreas/Pancreas_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Pancreas/Pancreas_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Pancreas/Pancreas_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Prostate/Prostate_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Prostate/Prostate_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Prostate/Prostate_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Stomach/Stomach_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Stomach/Stomach_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Stomach/Stomach_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Thyroid/Thyroid_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Thyroid/Thyroid_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Thyroid/Thyroid_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Uterus/Uterus_exomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/exomes/Uterus/Uterus_exomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/exomes/Uterus/Uterus_exomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/ALL/ALL_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/ALL/ALL_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/ALL/ALL_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/AML/AML_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/AML/AML_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/AML/AML_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Breast/Breast_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Breast/Breast_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Breast/Breast_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/CLL/CLL_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/CLL/CLL_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/CLL/CLL_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Liver/Liver_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Liver/Liver_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Liver/Liver_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Lung Adeno/Lung Adeno_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Lung Adeno/Lung Adeno_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Lung Adeno/Lung Adeno_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Lymphoma B-cell/Lymphoma B-cell_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Lymphoma B-cell/Lymphoma B-cell_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Lymphoma B-cell/Lymphoma B-cell_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Medulloblastoma/Medulloblastoma_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Medulloblastoma/Medulloblastoma_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Medulloblastoma/Medulloblastoma_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Pancreas/Pancreas_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Pancreas/Pancreas_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Pancreas/Pancreas_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Pilocytic Astrocytoma/Pilocytic Astrocytoma_genomes_mutational_catalog_192_subs_with_strand_bias.mat
data/2013-AlexandrovEtAl-Nature/genomes/Pilocytic Astrocytoma/Pilocytic Astrocytoma_genomes_mutational_catalog_96_subs.mat
data/2013-AlexandrovEtAl-Nature/genomes/Pilocytic Astrocytoma/Pilocytic Astrocytoma_genomes_mutational_catalog_99_subs_with_indels_and_dinucs.mat
example1.m
example2.m
example3.m
example4.m
input/100_WTSI_BRCA_whole_exome_substitutions_strand_bias.mat
input/21_WTSI_BRCA_whole_genome_substitutions.mat
license.txt
plotting/plotSamples.m
plotting/plotSamplesWithStrandBias.m
plotting/plotSignatures.m
plotting/plotSignaturesExposureInSamples.m
plotting/plotSignatureStabilityAndReconstruction.m
plotting/plotSignaturesWithStrandBias.m
plotting/rotateticklabel.m
plotting/rotateticklabelWithColor.m
plotting/ThousandSep.m
readme.pdf
source/addWeak.m
source/bootstrapCancerGenomes.m
source/decipherMutationalProcesses.m
source/deconvolute.m
source/evaluateStability.m
source/extract.m
source/fcnnls.m
source/filterOutIterations.m
source/gdcls.m
source/nmf.m
source/nmfsh_comb.m
source/removeWeak.m
__MACOSX/._data
__MACOSX/._example1.m
__MACOSX/._example2.m
__MACOSX/._example3.m
__MACOSX/._example4.m
__MACOSX/._input
__MACOSX/._output
__MACOSX/._plotting
__MACOSX/._source
__MACOSX/._temp
__MACOSX/data/2012-Nik-ZainalEtAl-Cell/._21_WTSI_BRCA_whole_genome_substitutions.mat
__MACOSX/data/2013-AlexandrovEtAl-CellReports/._100_WTSI_BRCA_whole_exome_substitutions.mat
__MACOSX/data/2013-AlexandrovEtAl-CellReports/._100_WTSI_BRCA_whole_exome_substitutions_strand_bias.mat
__MACOSX/data/2013-AlexandrovEtAl-CellReports/._21_WTSI_BRCA_whole_genome_substitutions.mat
__MACOSX/data/2013-AlexandrovEtAl-CellReports/._21_WTSI_BRCA_whole_genome_substitutions_dinucleotides_indels_kataegis.mat
__MACOSX/data/2013-AlexandrovEtAl-CellReports/._21_WTSI_BRCA_whole_genome_substitutions_pentanucleotides.mat
__MACOSX/data/2013-AlexandrovEtAl-CellReports/._21_WTSI_BRCA_whole_genome_substitutions_strand_bias.mat
__MACOSX/data/2013-AlexandrovEtAl-Nature/._.DS_Store
__MACOSX/input/._100_WTSI_BRCA_whole_exome_substitutions_strand_bias.mat
__MACOSX/input/._21_WTSI_BRCA_whole_genome_substitutions.mat
__MACOSX/plotting/._plotSamples.m
__MACOSX/plotting/._plotSamplesWithStrandBias.m
__MACOSX/plotting/._plotSignatures.m
__MACOSX/plotting/._plotSignaturesExposureInSamples.m
__MACOSX/plotting/._plotSignatureStabilityAndReconstruction.m
__MACOSX/plotting/._plotSignaturesWithStrandBias.m
__MACOSX/plotting/._rotateticklabel.m
__MACOSX/plotting/._rotateticklabelWithColor.m
__MACOSX/plotting/._ThousandSep.m
__MACOSX/source/._addWeak.m
__MACOSX/source/._bootstrapCancerGenomes.m
__MACOSX/source/._decipherMutationalProcesses.m
__MACOSX/source/._deconvolute.m
__MACOSX/source/._evaluateStability.m
__MACOSX/source/._extract.m
__MACOSX/source/._fcnnls.m
__MACOSX/source/._filterOutIterations.m
__MACOSX/source/._gdcls.m
__MACOSX/source/._nmf.m
__MACOSX/source/._nmfsh_comb.m
__MACOSX/source/._removeWeak.m

Contact us