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cancer-genomics x

17 search results found

Awesome Cancer Variant Databases ⭐ 284

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

Ideogram ⭐ 265

Chromosome visualization for the web

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Personal Cancer Genome Reporter (PCGR)

Microassembly based somatic variant caller for NGS data

Sigprofilerextractor ⭐ 132

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Sigprofilermatrixgenerator ⭐ 91

SigProfilerMatrixGenerator 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.

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

Genome Nexus ⭐ 38

Backend server for Genome Nexus

Sigprofilersimulator ⭐ 18

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Sigprofilermatrixgeneratorr ⭐ 17

R wrapper for utilizing the SigProfilerMatrixGenerator framework

Accucopy ⭐ 13

Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.

Sigprofilerextractorr ⭐ 11

An R wrapper for SigProfilerExtractor that allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

The Broad Institute Single Cell Rna Seq Data Set ⭐ 9

Visualize cancer genomes with FAIR single-cell RNA-seq data

A software to detect virome-wide integrations

Virtual Normal Correction ⭐ 6

Set of commandline tools for analysis of tumor variants without a matching normal. Method described in Genome Research: http://genome.cshlp.org/content/25/9/1382.full

Reference-free FASTQ filter for rare germline and somatic variants

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