228 skills found · Page 2 of 8
broadinstitute / Depmap OmicsWhat you need to process the Quarterly DepMap-Omics releases from Terra
SigProfilerSuite / SigProfilerMatrixGeneratorSigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
mdozmorov / Cancer NotesA continually expanding collection of cancer genomics notes and data
ropensci / UCSCXenaTools:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
GooglingTheCancerGenome / Sv CallersSnakemake-based workflow for detecting structural variants in genomic data
AmpliconSuite / AmpliconSuite PipelineA quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArchitect, and invokes AmpliconClassifier
FunGeST / PalimpsestAn R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
murphycj / AGFusionPython package to annotate and visualize gene fusions.
yifengtao / Genome TransformerPredicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer
iVis-at-Bilkent / Pathway MapperPathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
sigven / CpsrCancer Predisposition Sequencing Reporter (CPSR)
ding-lab / MuSiC2identifying mutational significance in cancer genomes
lynnlangit / TeamTeriBioinformatics on GCP, AWS or Azure
rhshah / IMPACT PipelineFramework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
broadinstitute / Gistic2Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
getzlab / DeTiNDeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
SigProfilerSuite / SigProfilerPlottingSigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.
BIMSBbioinfo / MauiMulti-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
BioinformaticsFMRP / TCGAWorkflowTCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
BIMSBbioinfo / IkarusIdentifying tumor cells at the single-cell level using machine learning
