96 Open source projects that are alternatives of or similar to civic-client

Backend Server for CIViC Project

A Slicer extension to provide a GUI around pyradiomics

Genomics using open source tools, running on GCP or AWS

Cancer Predisposition Sequencing Reporter (CPSR)

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Lightweight DICOMweb Server with CouchDB

Cancer-dedicated gene set interpretation

A phenotype-based tool for variant prioritization in WES and WGS data

CNN histopathologic tumor identifier.

(WIP) best-practices workflow for rare disease

A basic framework for pulmonary nodule detection and characterization in CT

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.

pathoscore evaluates variant pathogenicity tools and scores.

Text mining cancer biomarkers for the CIVIC database

Ordo: A minimalist language with row polymorphism

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.

TCGA data acquisition and processing for Project Cognoma

Blazor component library for FluentUI. Microsoft's official lightweight wrapper around the FluentUI Web Components for use with .NET 6.0 Blazor applications

A novel management, annotation, and machine learning framework for analyzing cancer mutations

REVOLVER - Repeated Evolution in Cancer

Fast and accurate gene fusion detection from RNA-Seq data

simple viewer for variant call format using htslib

PEPPER-Margin-DeepVariant

Harbol is a collection of data structure and miscellaneous libraries, similar in nature to C++'s Boost, STL, and GNOME's GLib

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Backend server for Genome Nexus

Every traffic violation in the city of Philadelphia issued from 2006 to 2014

Quick test using JWT authentication for a blazor hosted (Client/Serverside) app with API and Authentication.

Numerical Encoding for Human Genetic Variants

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Spark VCF data source implementation for Dataframes

A Python-Tensorflow neural network for classifying cancer data

Bioconductor package for management of multi-assay data

Natural-JS : Javascript Front-End Architecture Framework

A simple and mobile-friendly HTML5 template with CastleCSS to kickstart your website

😃 A functional reactive programming (FRP) demo created with PureScript events and behaviors.

VariantRetriever is a minimalist package for feature flagging

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Multi-sample somatic variant caller

List of IARC bioinformatics nextflow pipelines

📊Evaluating, filtering, comparing, and visualising VCF

A repository for open source civic tools from many countries and organizations

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.

Variant types in TypeScript

Simple tagged unions

Lollipop-diagram to interactively visualize genetic mutations

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

Gene fusion detection and visualization

ACCESS NYC Pattern library and design system documentation for https://access.nyc.gov. Maintained by @NYCOpportunity

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

Node.js client library for the Civic Secure Identity Platform (SIP).

An interactive web portal for exploring immuno-oncology data

🚀 Handy dynamic styles utilities for React Native and React Native Web.

VTK.js image viewport component in React

Multi-task deep learning framework for multi-omics data analysis

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 SigProfilerMatrixGen…

Provide R access to the NCI Genomic Data Commons portal.

3D hotspot mutation proximity analysis tool