Mark Cowley
Precision Oncology for Childhood Cancer
X
X
Bluesky
Bluesky
LinkedIn
LinkedIn
Email
Email
GitHub
GitHub
Website
Website
Cancer Bioinformatics Tools
nf-core/oncoanalyser: A comprehensive cancer DNA/RNA analysis and reporting pipeline
nf-core/oncoanalyser: A comprehensive cancer DNA/RNA analysis and reporting pipeline
A comprehensive cancer DNA/RNA analysis and reporting pipeline - nf-core/oncoanalyser
nf-carbonite: Comprehensive cancer RNAseq analysis pipeline
nf-carbonite: Comprehensive cancer RNAseq analysis pipeline
Contribute to CCICB/nf-carbonite development by creating an account on GitHub.
Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology
Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology
LINX: unscramble cancer genomes (Hartwig)
LINX: unscramble cancer genomes (Hartwig)
Various algorithms for analysing genomics data. Contribute to hartwigmedical/hmftools development by creating an account on GitHub.
WISP: tumour fraction estimation from tumour-informed ctDNA analysis (Hartwig)
WISP: tumour fraction estimation from tumour-informed ctDNA analysis (Hartwig)
Various algorithms for analysing genomics data. Contribute to hartwigmedical/hmftools development by creating an account on GitHub.
CIDER: extract Ig/Tcr CDR3 sequences from WGS for MRD (Hartwig)
CIDER: extract Ig/Tcr CDR3 sequences from WGS for MRD (Hartwig)
Various algorithms for analysing genomics data. Contribute to hartwigmedical/hmftools development by creating an account on GitHub.
vcf2mafR: Convert VCFs and VCF-related formats to MAF
vcf2mafR: Convert VCFs and VCF-related formats to MAF
sigverse: Simplifying mutational signature analysis in R
sigverse: Simplifying mutational signature analysis in R
methyliser: EPIC array methylation levels
methyliser: EPIC array methylation levels
micrite: characterising microbes from cancer WGS data
micrite: characterising microbes from cancer WGS data
ggoncoplot: easily create interactive oncoplots
ggoncoplot: easily create interactive oncoplots
ggEDA: exploratory data visualisations in R
ggEDA: exploratory data visualisations in R
GitHub repo
GitHub repo
Bitbucket repo
Bitbucket repo
ZERO cloud
ZeroDash (login required)
ZeroDash (login required)
A web portal to improve the efficiency of a curation scientist's workflow
MTBnotes: childhood cancer knowledgebase (login required)
MTBnotes: childhood cancer knowledgebase (login required)
Web site created using create-react-app
ZERO Childhood Cancer Data Portal
ZERO Childhood Cancer Data Portal
Splicing
Data-driven insights to inform splice-altering variant assessment
Data-driven insights to inform splice-altering variant assessment
Predicting the functional consequences of a putative splice-altering variant (SAV) is challenging. Here, we present a comprehensive framework for evaluating SAVs and predicting their functional consequences. It is grounded in known splicing rules and helps bridge the gap between in silico predictions and pathogenicity assessment.
Introme (GitHub)
Introme (GitHub)
Introme prioritises coding and noncoding splice-altering variants for clinical variant interpretation - CCICB/introme
SpliceVarDB
SpliceVarDB
SAVvy (alpha)
SAVvy (alpha)
Academic Profiles
Computational Biology Group - CCIA
Computational Biology Group - CCIA
Scopus Profile
Scopus Profile
TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
ORCID
ORCID
Google Scholar
Google Scholar
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