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Update signature_doc.rst
Updates to motif_doc.rst
Latest from upstream
Rank menu logic changed: - only input file is required - input format is a multisampled MAF file - profile, cohort_size and observed mutations would be extracted from input file - the file is actually processed twice: once for nucleic acid mutations and once for protein mutations, the overhead is small - if cohort is requested -c will give a list of available precalculated Mutagene cohorts (based on COSMIC data) - if cohort is specified it will override profile, cohort_size and observed mutations - it is possible to override profile and cohort_size separately Only the first encountered transcript for a gene is considered. Mutations in other transcripts would be ignored in the analysis. This is important to avoid overcounting of observed mutations in MAF files with per-transcript annotation of mutations. Currently pseudo-counts are no longer added to observed mutations data even if precalculated cohort is used. This changes results compared to previous implementation.
* Added handling of 404 error in case an invalid cohort is provided for MSKCC
Bumps [cryptography](https://github.com/pyca/cryptography) from 2.9 to 3.2. - [Release notes](https://github.com/pyca/cryptography/releases) - [Changelog](https://github.com/pyca/cryptography/blob/master/CHANGELOG.rst) - [Commits](pyca/cryptography@2.9...3.2) Signed-off-by: dependabot[bot] <[email protected]>
Bump cryptography from 2.9 to 3.2
Rank/without cohort
Merge upstream following merge from docs
Feature/51 remove rank vcf
Hotfix/cli test fetch
Hotfix/cli test fetch
Bumps [cryptography](https://github.com/pyca/cryptography) from 3.2 to 3.3.2. - [Release notes](https://github.com/pyca/cryptography/releases) - [Changelog](https://github.com/pyca/cryptography/blob/master/CHANGELOG.rst) - [Commits](pyca/cryptography@3.2...3.3.2) Signed-off-by: dependabot[bot] <[email protected]>
…locus in the transcript
Bump cryptography from 3.2 to 3.3.2
add support for ranking silent mutations given MAF (e.g. L61=)
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