Topic: cancer-genomics Goto Github

👇 Here are 263 public repositories matching this topic...

alexandrovlab / sigprofilerextractor
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
bioinformatics somatic-variants cancer-genomics mutational-signatures mutation-analysis

alexandrovlab / sigprofilermatrixgenerator
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
mutational-signatures somatic-variants bioinformatics cancer-genomics mutation-analysis

alexandrovlab / sigprofilermatrixgeneratorr
cancer-genomics,R wrapper for utilizing the SigProfilerMatrixGenerator framework
Organization: alexandrovlab
bioinformatics somatic-variants cancer-genomics mutation-analysis mutational-signatures

alexandrovlab / sigprofilerplotting
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
somatic-variants cancer-genomics mutational-signatures mutation-analysis visualization

ampliconsuite / ampliconsuite-pipeline
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 cancer-genomics ecdna

bimsbbioinfo / ikarus
cancer-genomics,Identifying tumor cells at the single-cell level using machine learning
Organization: bimsbbioinfo
bioinformatics cancer-genomics machine-learning single-cell

bimsbbioinfo / maui
cancer-genomics,Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Organization: bimsbbioinfo
bioinformatics deep-learning autoencoder latent-factor-model cancer-genomics multi-omics

bioinform / somaticseq
cancer-genomics,An ensemble approach to accurately detect somatic mutations using SomaticSeq
Organization: bioinform
Home Page: http://bioinform.github.io/somaticseq/
somatic-variants cancer-genomics

brentp / somalier
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 bioinformatics genomics

broadinstitute / depmap_omics
cancer-genomics,What you need to process the Quarterly DepMap-Omics releases from Terra
Organization: broadinstitute
Home Page: https://depmap.org/portal/
depmap cancer-genomics cloud-computing data-science

cansysbio / consensustme
cancer-genomics,ConsensusTME Gene Sets and R Script
Organization: cansysbio
cancer-genomics bioinformatics-pipeline deconvolution immune tumour-microenvironment consensus-algorithm

caravagnalab / revolver
cancer-genomics,REVOLVER - Repeated Evolution in Cancer
Organization: caravagnalab
Home Page: https://caravagnalab.github.io/revolver/
cancer-evolution cancer-genomics clustering phylogenetic-trees transfer-learning

cbg-ethz / scicone
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
bayesian-inference single-cell copy-number-variation cancer-genomics mcmc

cbioportal / cbioportal
cancer-genomics,cBioPortal for Cancer Genomics
Organization: cbioportal
Home Page: https://cbioportal.org
cancer-genomics science visualization precision-medicine

cbioportal / cbioportal-frontend
cancer-genomics,React Frontend of cBioPortal :tada:
Organization: cbioportal
Home Page: https://cbioportal.org
react mobx cancer-genomics

cmuschwartzlab / cancer-phylogenetics-prognostic-prediction
cancer-genomics,Improving Personalized Prediction of Cancer Prognoses with Clonal Evolution Models
Organization: cmuschwartzlab
evolutionary-models survival-analysis survival-prediction cancer-genomics cancer-prognoses

crazyhottommy / getting-started-with-genomics-tools-and-resources
cancer-genomics,Unix, R and python tools for genomics and data science
User: crazyhottommy
cancer-genomics bioinformatics data-science

dellytools / delly
cancer-genomics,DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Organization: dellytools
structural-variation sv-discovery delly-users delly rearrangement genomic cancer-genomics germline tumor svs

ding-lab / msisensor
cancer-genomics,microsatellite instability detection using tumor only or paired tumor-normal data
Organization: ding-lab
msi cancer-genomics msi-score bam-files

ding-lab / music2
cancer-genomics,identifying mutational significance in cancer genomes
Organization: ding-lab
smg mutation-relation clinical-correlation cancer-genomics pfam-annotation

eweitz / ideogram
cancer-genomics,Chromosome visualization for the web
User: eweitz
Home Page: https://eweitz.github.io/ideogram
visualization genomics cytogenetics karyotype cancer-genomics comparative-genomics personal-genomics

fungest / palimpsest
cancer-genomics,An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
User: fungest
cancer-genomics genomics visualization r somatic-mutations mutational-signatures structural-variation clonality tumor-heterogeneity tumor-evolution

genome-nexus / genome-nexus
cancer-genomics,Backend server for Genome Nexus
Organization: genome-nexus
Home Page: https://genomenexus.org
cancer-genomics rest-api knowledgebase

genome-spy / genome-spy
cancer-genomics,A visualization grammar and GPU-accelerated toolkit for genomic data
Organization: genome-spy
Home Page: http://genomespy.app/
webgl visualization bioinformatics genome-visualization graphics data-visualization visual-analytics cancer-genomics genome

gerstung-lab / basiss
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 spatial-transcriptomics

getzlab / detin
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 cancer-variants cancer-genome-atlas tumor detection tumor-in-normal somatic-mutations tin

googlingthecancergenome / sv-callers
cancer-genomics,Snakemake-based workflow for detecting structural variants in genomic data
Organization: googlingthecancergenome
Home Page: https://research-software.nl/software/sv-callers
bioinformatics cancer-genomics germline-variants hpc-applications snakemake somatic-variants structural-variants sv-calling wgs workflow

greenelab / tybalt
cancer-genomics,Training and evaluating a variational autoencoder for pan-cancer gene expression data
Organization: greenelab
cancer-genomics deep-learning unsupervised-learning gene-expression variational-autoencoder script tool analysis autoencoder variational-autoencoders

griffithlab / civic-client
cancer-genomics,Web client for CIViC: Clinical Interpretations of Variants in Cancer
Organization: griffithlab
nci-itcr civic javascript front-end-framework cancer cancer-genomics variants

griffithlab / civic-server
cancer-genomics,Backend Server for CIViC Project
Organization: griffithlab
nci-itcr ruby civic backend-server cancer cancer-genomics variants

hw538 / cfdnapro
cancer-genomics,cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
User: hw538
cell-free-dna genomics-visualization swgs whole-genome-sequencing liquid-biopsy cancer-genomics cancer-research early-detection bioinformatics r

ivis-at-bilkent / pathway-mapper
cancer-genomics,PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Organization: ivis-at-bilkent
Home Page: https://www.pathwaymapper.org/
systems-biology pathways pathway-analysis cancer-pathways cancer-genomics network-visualization tcga bioinformatics graphviz

joiningdata / lollipops
cancer-genomics,Lollipop-style mutation diagrams for annotating genetic variations.
Organization: joiningdata
go cancer-variants cancer-genomics visualization diagram

kharchenkolab / numbat
cancer-genomics,Haplotype-aware CNV analysis from single-cell RNA-seq
Organization: kharchenkolab
Home Page: https://kharchenkolab.github.io/numbat/
cancer-genomics cnv-detection single-cell phylogeny single-cell-analysis single-cell-rna-seq spatial-transcriptomics lineage-tracing

kieranrcampbell / clonealign
cancer-genomics,Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
User: kieranrcampbell
single-cell gene-expression cancer-genomics

lynnlangit / teamteri
cancer-genomics,Bioinformatics on GCP, AWS or Azure
User: lynnlangit
cancer-genomics variants genome-analysis genome-sequencing gcp aws variant-calls bioinformatics genomics-analysis gatk azure

murphycj / agfusion
cancer-genomics,Python package to annotate and visualize gene fusions.
User: murphycj
Home Page: https://www.agfusion.app
gene-fusion protein fusion rna-seq python cancer cancer-genomics chimera bioinformatics structural-variation

nygenome / lancet
cancer-genomics,Microassembly based somatic variant caller for NGS data
Organization: nygenome
somatic-mutations cancer-genomics variant-callers debruijn-graph snvs indels local-assembly

poisonalien / maftools
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
bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga

poisonalien / somaticfreq
cancer-genomics,knowledge-based genotyping of cancer hotspots from the tumor BAM files
User: poisonalien
bam-files cancer-genomics html-report somatic-mutations

rezacsedu / multimodal-autoencoder-for-breast-cancer
cancer-genomics,Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data
User: rezacsedu
multimodality multimodal-autoencoder cancer-genomics tcga-data neural-networks deep-learning survival-prediction classification regression

rhshah / impact-pipeline
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
ngs cancer-genomics precision-medicine cancer-variants illumina-sequencing mskimpact msk-impact

seandavi / awesome-cancer-variant-databases
cancer-genomics,A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
User: seandavi
awesome-list cancer cancer-variants cancer-genomics mutations clinical-trials bioinformatics

shixiangwang / variants2neoantigen
cancer-genomics,A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
User: shixiangwang
cancer-genomics neoantigen maf vcf

sigven / cacao
cancer-genomics,Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
User: sigven
alignment bam cancer cancer-genomics clinical-decision-support command-line-tool coverage-report next-generation-sequencing pathogenic-loci pathogenic-variants quality-assurance quality-control sequencing sequencing-coverage

sigven / cpsr
cancer-genomics,Cancer Predisposition Sequencing Reporter (CPSR)
User: sigven
Home Page: https://sigven.github.io/cpsr/
acmg cancer cancer-genomics cancer-predisposition cancer-predisposition-report cancer-research docker genomics-england-panelapp germline-variants inherited pathogenic-loci pathogenic-variants pathogenicity predisposition report-generator reporting-tool vcf workflow-engine

sigven / pcgr
cancer-genomics,Personal Cancer Genome Reporter (PCGR)
User: sigven
Home Page: https://sigven.github.io/pcgr
cancer-genomics cancer-variants somatic interpreter reporting-engine clinical oncology-data precision-oncology vcf tumor

tariqdaouda / pygeno
cancer-genomics,Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
User: tariqdaouda
Home Page: http://pygeno.iric.ca
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical

umccr / umccrise
cancer-genomics,:snake: DRAGEN Tumor/Normal workflow post-processing
Organization: umccr
Home Page: https://umccr.github.io/umccrise/
pipeline bcbio reporting cancer-genomics variant-calls bcbio-nextgen cancer-report umccrise pcgr

wittelab / orchid
cancer-genomics,A novel management, annotation, and machine learning framework for analyzing cancer mutations
Organization: wittelab
bioinformatics machine-learning cancer-genomics variant-annotations