Awesome Open Source
Search
Programming Languages
Languages
All Categories
Categories
About
Search results for cancer genomics
cancer-genomics
x
109 search results found
Getting Started With Genomics Tools And Resources
⭐
991
Unix, R and python tools for genomics and data science
Cbioportal
⭐
535
cBioPortal for Cancer Genomics
Maftools
⭐
400
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Delly
⭐
397
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
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
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Pcgr
⭐
234
Personal Cancer Genome Reporter (PCGR)
Somalier
⭐
224
fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
Somaticseq
⭐
185
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Lollipops
⭐
175
Lollipop-style mutation diagrams for annotating genetic variations.
Genome Spy
⭐
150
A visualization grammar and GPU-accelerated toolkit for genomic data
Lancet
⭐
145
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.
Numbat
⭐
122
Haplotype-aware CNV analysis from single-cell RNA-seq
Tybalt
⭐
107
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Msisensor
⭐
99
microsatellite instability detection using tumor only or paired tumor-normal data
Cbioportal Frontend
⭐
92
React Frontend of cBioPortal 🎉
Depmap_omics
⭐
91
What you need to process the Quarterly DepMap-Omics releases from Terra
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.
Music2
⭐
56
identifying mutational significance in cancer genomes
Palimpsest
⭐
56
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Revolver
⭐
53
REVOLVER - Repeated Evolution in Cancer
Pathway Mapper
⭐
52
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Sv Callers
⭐
52
Snakemake-based workflow for detecting structural variants in genomic data
Cpsr
⭐
50
Cancer Predisposition Sequencing Reporter (CPSR)
Teamteri
⭐
50
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
Civic Client
⭐
49
Web client for CIViC: Clinical Interpretations of Variants in Cancer
Detin
⭐
48
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Ampliconsuite Pipeline
⭐
48
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
Maui
⭐
47
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
Impact Pipeline
⭐
47
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Agfusion
⭐
46
Python package to annotate and visualize gene fusions.
Sevenbridges Python
⭐
44
SevenBridges Python Api bindings
Sigprofilerplotting
⭐
43
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.
Civic Server
⭐
39
Backend Server for CIViC Project
Genome Nexus
⭐
38
Backend server for Genome Nexus
Ikarus
⭐
34
Identifying tumor cells at the single-cell level using machine learning
Cbioportaldata
⭐
29
Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
Orchid
⭐
29
A novel management, annotation, and machine learning framework for analyzing cancer mutations
Sevenbridges R
⭐
27
Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R
Clonealign
⭐
25
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
Cacao
⭐
22
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Cfdnapro
⭐
20
cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
Scicone
⭐
20
Single-cell copy number calling and event history reconstruction.
Civic V2
⭐
18
CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer
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.
Cgdsr
⭐
18
R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS)
Ngcgh
⭐
17
Tools for producing pseudo-cgh of next-generation sequencing data
Cancerdiscover
⭐
17
Open-source software pipeline for cancer classification from high-throughput data using machine learning.
Sigprofilermatrixgeneratorr
⭐
17
R wrapper for utilizing the SigProfilerMatrixGenerator framework
Lorax
⭐
16
A long-read analysis toolbox for cancer and population genomics
Okapi
⭐
16
Recipes and Tutorials for Automation & Extension on the CGC and SBPLAT platforms
Neural Ensemble Method For Cancer Prediction
⭐
15
A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations
Biocancer
⭐
15
♋ 🆓 A Shiny App for Interactive Multi-OMICS Cancer Data Visualization and analysis
Umccrise
⭐
14
🐍 DRAGEN Tumor/Normal workflow post-processing
Variants2neoantigen
⭐
14
a neoantigen calling pipeline begins from variants record file (MAF)
Ampliconreconstructorom
⭐
14
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
Accucopy
⭐
13
Accucopy is a computational method that infers Allele-specific Copy Number alterations from low-coverage low-purity tumor sequencing Data.
Sigprofilertopography
⭐
13
SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.
Mimsi
⭐
12
Microsatellite Instability Classification using Multiple Instance Learning
Cancer_data
⭐
11
A unified downloader+preprocessor for cancer genomics datasets
Scatrex
⭐
11
Map single-cell transcriptomes to copy number evolutionary trees.
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.
Basiss
⭐
11
Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper
Canceromicsnet
⭐
10
A Graph Neural Network Model for prediction of the effectiveness of a drug on a given cancer cell lines
Ectmb
⭐
10
The Broad Institute Single Cell Rna Seq Data Set
⭐
9
Visualize cancer genomes with FAIR single-cell RNA-seq data
Bioconcotk
⭐
9
Bioconductor components for general cancer genomics
Htan Portal
⭐
8
The HTAN Data Portal
Somaticfreq
⭐
8
knowledge-based genotyping of cancer hotspots from the tumor BAM files
Omitrans
⭐
8
The first GANs-based omics-to-omics translation framework
Sigprofilerclusters
⭐
8
Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and non-clustered groups on a sample-dependent basis.
Webgen
⭐
8
WebGen Vertically Integrated Project
Pc_cna_signature
⭐
8
Prostate Cancer Alteration Signature Analysis
Biostan
⭐
8
Materials for BioC-2016 workshop entitled "Introduction to Bayesian Inference using Stan with Applications to Cancer Genomics"
Consensustme
⭐
8
ConsensusTME Gene Sets and R Script
Vicaller
⭐
8
A software to detect virome-wide integrations
Oncothreads
⭐
8
OncoThreads longitudinal cancer genomics visualization project.
Gpgr
⭐
8
📚 Genomics Platform Group Reporter
Access Pipeline
⭐
7
cfDNA Sequencing Pipeline with UMI
Curatedpcadata
⭐
7
Curated Prostate Cancer Data R-package
Scnova
⭐
7
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
Scarlet
⭐
7
SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.
Ucsc Xena Server
⭐
7
Turn-key functional genomics data server.
Cross_svm
⭐
7
faster and simpler version of SVM learning software libsvm
Multimodal Autoencoder For Breast Cancer
⭐
7
Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data
Guidescan Web
⭐
6
A guideRNA design tool for the modern era.
Camutqc
⭐
6
An R package for mutation quality control of cancer genomic sequening dataset
Onconetexplainer
⭐
6
OncoNetExplainer: Explainable Prediction of Cancer Types Based on Gene Expression Data
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
Svparser
⭐
6
Explore and filter structural variant calls from Lumpy and Delly VCF files
Tidyestimate
⭐
6
ESTIMATE tumor infiltration, the tidy way
Gsinghal_python_src
⭐
6
Python Code, Machine Learning, Cancer Genomics, DNA/RNA Sequence Analysis
Geneoncox
⭐
6
Human gene annotations for the oncology domain
Nowellpack
⭐
6
Blang library for cancer genomics
Fings
⭐
6
Filters for Next Generation Sequencing
Geno4sd
⭐
6
An python omics data toolkit for the analysis across biological scales
Hgg Oncohistones
⭐
5
Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)
Sigrap
⭐
5
🎶 Wrappers for somatic mutation signature analysis tools
1-100 of 109 search results
Next >
Privacy
|
About
|
Terms
|
Follow Us On Twitter
Copyright 2018-2024 Awesome Open Source. All rights reserved.