Topic: cancer-genomics Goto Github
Some thing interesting about cancer-genomics
Some thing interesting about cancer-genomics
cancer-genomics,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.
Organization: alexandrovlab
cancer-genomics,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.
Organization: alexandrovlab
cancer-genomics,R wrapper for utilizing the SigProfilerMatrixGenerator framework
Organization: alexandrovlab
cancer-genomics,SigProfilerPlotting 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.
Organization: alexandrovlab
cancer-genomics,A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
Organization: ampliconsuite
cancer-genomics,Identifying tumor cells at the single-cell level using machine learning
Organization: bimsbbioinfo
cancer-genomics,Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Organization: bimsbbioinfo
cancer-genomics,An ensemble approach to accurately detect somatic mutations using SomaticSeq
Organization: bioinform
Home Page: http://bioinform.github.io/somaticseq/
cancer-genomics,fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
User: brentp
cancer-genomics,What you need to process the Quarterly DepMap-Omics releases from Terra
Organization: broadinstitute
Home Page: https://depmap.org/portal/
cancer-genomics,ConsensusTME Gene Sets and R Script
Organization: cansysbio
cancer-genomics,REVOLVER - Repeated Evolution in Cancer
Organization: caravagnalab
Home Page: https://caravagnalab.github.io/revolver/
cancer-genomics,Single-cell copy number calling and event history reconstruction.
Organization: cbg-ethz
Home Page: https://www.biorxiv.org/content/10.1101/2020.04.28.065755v1
cancer-genomics,cBioPortal for Cancer Genomics
Organization: cbioportal
Home Page: https://cbioportal.org
cancer-genomics,React Frontend of cBioPortal :tada:
Organization: cbioportal
Home Page: https://cbioportal.org
cancer-genomics,Improving Personalized Prediction of Cancer Prognoses with Clonal Evolution Models
Organization: cmuschwartzlab
cancer-genomics,Unix, R and python tools for genomics and data science
User: crazyhottommy
cancer-genomics,DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Organization: dellytools
cancer-genomics,identifying mutational significance in cancer genomes
Organization: ding-lab
cancer-genomics,Chromosome visualization for the web
User: eweitz
Home Page: https://eweitz.github.io/ideogram
cancer-genomics,An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
User: fungest
cancer-genomics,Backend server for Genome Nexus
Organization: genome-nexus
Home Page: https://genomenexus.org
cancer-genomics,A visualization grammar and GPU-accelerated toolkit for genomic data
Organization: genome-spy
Home Page: http://genomespy.app/
cancer-genomics,Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
Organization: gerstung-lab
Home Page: https://doi.org/10.1038/s41586-022-05425-2
cancer-genomics,DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Organization: getzlab
cancer-genomics,Snakemake-based workflow for detecting structural variants in genomic data
Organization: googlingthecancergenome
Home Page: https://research-software.nl/software/sv-callers
cancer-genomics,Training and evaluating a variational autoencoder for pan-cancer gene expression data
Organization: greenelab
cancer-genomics,Web client for CIViC: Clinical Interpretations of Variants in Cancer
Organization: griffithlab
cancer-genomics,Backend Server for CIViC Project
Organization: griffithlab
cancer-genomics,cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
User: hw538
cancer-genomics,PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Organization: ivis-at-bilkent
Home Page: https://www.pathwaymapper.org/
cancer-genomics,Lollipop-style mutation diagrams for annotating genetic variations.
Organization: joiningdata
cancer-genomics,Haplotype-aware CNV analysis from single-cell RNA-seq
Organization: kharchenkolab
Home Page: https://kharchenkolab.github.io/numbat/
cancer-genomics,Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
User: kieranrcampbell
cancer-genomics,Bioinformatics on GCP, AWS or Azure
User: lynnlangit
cancer-genomics,Python package to annotate and visualize gene fusions.
User: murphycj
Home Page: https://www.agfusion.app
cancer-genomics,Microassembly based somatic variant caller for NGS data
Organization: nygenome
cancer-genomics,Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
User: poisonalien
Home Page: http://bioconductor.org/packages/release/bioc/html/maftools.html
cancer-genomics,knowledge-based genotyping of cancer hotspots from the tumor BAM files
User: poisonalien
cancer-genomics,Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data
User: rezacsedu
cancer-genomics,Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
User: rhshah
Home Page: http://impact-pipeline.readthedocs.org/en/latest/index.html
cancer-genomics,A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
User: seandavi
cancer-genomics,A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
User: shixiangwang
cancer-genomics,Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
User: sigven
cancer-genomics,Cancer Predisposition Sequencing Reporter (CPSR)
User: sigven
Home Page: https://sigven.github.io/cpsr/
cancer-genomics,Personal Cancer Genome Reporter (PCGR)
User: sigven
Home Page: https://sigven.github.io/pcgr
cancer-genomics,Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
User: tariqdaouda
Home Page: http://pygeno.iric.ca
cancer-genomics,:snake: DRAGEN Tumor/Normal workflow post-processing
Organization: umccr
Home Page: https://umccr.github.io/umccrise/
cancer-genomics,A novel management, annotation, and machine learning framework for analyzing cancer mutations
Organization: wittelab
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