GitHub topics: genomics-visualization

Repositories

ucscGenomeBrowser/kent

UCSC Genome Browser source tree. Stable branch: "beta".

Language: C - Size: 569 MB - Last synced at: about 20 hours ago - Pushed at: about 21 hours ago - Stars: 236 - Forks: 93

neuhausi/canvasxpress-js

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Language: CSS - Size: 39.5 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 8 - Forks: 0

MaximilianStammnitz/ABA_receptor

Companion scripts for DMS data processing, dose-response curve fitting and figure reproduction (Stammnitz & Lehner, biorXiv 2025)

Language: R - Size: 30.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 1

snystrom/vplot

A commandline tool for generating vplot matrices from paired end sequencing data such as MNase-seq, ATAC-seq, or CUT&RUN.

Language: Rust - Size: 134 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2 - Forks: 1

DatViseR/Vivid-Volcano

A shiny app for custom analyzes of preprocessed omics data

Language: HTML - Size: 28.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 1

wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

Language: JavaScript - Size: 124 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 284 - Forks: 113

BodduSriPavan-111/kitikiplot

KitikiPlot A Python library to visualize categorical sliding window data

Language: Python - Size: 14.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 12 - Forks: 1

CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: TypeScript - Size: 200 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 94 - Forks: 42

thackl/gggenomes

A grammar of graphics for comparative genomics

Language: R - Size: 111 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 682 - Forks: 67

bernatgel/karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Language: R - Size: 3.08 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 315 - Forks: 41

satoshikawato/gbdraw

A genome diagram generator for microbes and organelles

Language: Python - Size: 557 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 5 - Forks: 3

hw538/cfDNAPro

cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

Language: R - Size: 2.96 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 31 - Forks: 5

lehner-lab/ABA_receptor Fork of MaximilianStammnitz/ABA_receptor

Companion scripts for DMS data processing, dose-response curve fitting and figure reproduction ("The genetic architecture of an allosteric hormone receptor", Stammnitz & Lehner, biorXiv 2025)

Language: R - Size: 30.5 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0

moshi4/pyGenomeViz

A genome visualization python package for comparative genomics

Language: Python - Size: 74.9 MB - Last synced at: 14 days ago - Pushed at: about 1 month ago - Stars: 330 - Forks: 21

moshi4/pyCirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

Language: Python - Size: 55.8 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 880 - Forks: 52

jasonwong-lab/gghic

gghic

Language: R - Size: 40.1 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 5 - Forks: 0

arvkevi/ezancestry

Easy genetic ancestry predictions in Python

Language: Jupyter Notebook - Size: 24.9 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 66 - Forks: 11

nschan/syri_gggenomes

Plot SyRi output via gggenomes

Language: R - Size: 5.69 MB - Last synced at: 30 days ago - Pushed at: 2 months ago - Stars: 2 - Forks: 0

robotoD/GenoVi

GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

Language: Python - Size: 175 MB - Last synced at: 15 days ago - Pushed at: almost 2 years ago - Stars: 94 - Forks: 12

tobiasrausch/vc

A tutorial on structural variant calling for short read sequencing data

Language: R - Size: 111 KB - Last synced at: 26 days ago - Pushed at: 8 months ago - Stars: 35 - Forks: 3

bigomics/omicsplayground

Visual self-service analytics platform for big omics data.

Language: R - Size: 1.2 GB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 125 - Forks: 36

xinglab-ai/genomap

Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)

Language: Python - Size: 43.7 MB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 3

VizCNV is an interactive tool designed to analyze and visualize CNVs from short read WGS data in rare disease research. Built on R Studio Shiny, it streamlines the identification of complex genomic rearrangements and facilitates advancements in understanding and diagnosing rare genetic conditions.

Language: R - Size: 138 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 2

mixOmicsTeam/mixOmics

Development repository for the Bioconductor package 'mixOmics '

Language: R - Size: 16.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 192 - Forks: 61

moshi4/GBKviz 📦

Easy-to-use web application for visualization and comparison of genomes in Genbank file

Language: Python - Size: 5.25 MB - Last synced at: 26 days ago - Pushed at: about 3 years ago - Stars: 21 - Forks: 4

PacificBiosciences/SVTopo

Complex structural variant visualization for HiFi sequencing data

Language: HTML - Size: 115 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 26 - Forks: 2

thierrygosselin/radiator

RADseq Data Exploration, Manipulation and Visualization using R

Language: HTML - Size: 11 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 59 - Forks: 23

daler/trackhub

create, manage, and upload track hubs for use in the UCSC genome browser

Language: Python - Size: 13.3 MB - Last synced at: 29 days ago - Pushed at: about 1 year ago - Stars: 54 - Forks: 20

IPK-BIT/divbrowse

A web application for interactive visualization and exploratory data analysis of variant call matrices

Language: Svelte - Size: 2.6 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 19 - Forks: 3

kdyrhage/GenomicMaps.jl

Julia package for visualising genomic data

Language: Julia - Size: 2.5 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 2

nf-core/hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Language: Nextflow - Size: 5.11 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 25 - Forks: 7

ccneko/OMACASE

an open-source (GPLv3) standalone Python package to analyze optical mapping data, with de novo repeat motif detection and analysis capabilities

Language: Python - Size: 2.74 MB - Last synced at: 14 days ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

GMOD/jbrowse-jupyter

A python package for showing JBrowse views

Language: Python - Size: 6.45 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 24 - Forks: 4

thierrygosselin/stackr

stackr: an R package to run stacks software pipeline

Language: HTML - Size: 20.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 29 - Forks: 8

czheluo/Circos-Pipeline

circos pipeline

Language: Perl - Size: 37.7 MB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 20 - Forks: 14

hoffmangroup/segway

Application for semi-automated genomic annotation.

Language: Shell - Size: 31 MB - Last synced at: 2 months ago - Pushed at: 11 months ago - Stars: 16 - Forks: 7

biojs/generator-biojs-webcomponents 📦

Generate all the boilerplate for your next BioJS tool!

Language: JavaScript - Size: 422 KB - Last synced at: 4 days ago - Pushed at: about 4 years ago - Stars: 10 - Forks: 3

gosling-lang/gosling-website

Documentation website of Gosling

Language: MDX - Size: 36.7 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 4 - Forks: 5

node/awesome-circos

A curated list of amazingly awesome Circos resources

Size: 5.86 KB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0

moshi4/MGCplotter 📦

Microbial Genome Circular plotting tool for comparative genomics using Circos

Language: Python - Size: 68.1 MB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 38 - Forks: 7

peaselab/mvftools

Language: Python - Size: 846 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 1

outbreak-info/python-outbreak-info

Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info

Language: Jupyter Notebook - Size: 31.4 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 6 - Forks: 2

stevekm/IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

Language: Python - Size: 26.4 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 140 - Forks: 50

G3viz/g3viz

Lollipop-diagram to interactively visualize genetic mutations

Language: JavaScript - Size: 65.2 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 31 - Forks: 19

gluesolutions/glue-genes

glue for genomics and transcriptomics

Language: Python - Size: 13.3 MB - Last synced at: 17 days ago - Pushed at: 5 months ago - Stars: 7 - Forks: 2

brentp/jigv

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Language: Nim - Size: 237 MB - Last synced at: 3 months ago - Pushed at: almost 2 years ago - Stars: 126 - Forks: 7

cidm-ph/phylepic

Epidemic curve + phylogenomic tree

Language: R - Size: 15.9 MB - Last synced at: 24 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

AABoyles/MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

Language: HTML - Size: 68.5 MB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 12 - Forks: 42

w-gao/pgv

A web-based, interactive pangenome visualization tool

Language: TypeScript - Size: 1.15 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 21 - Forks: 0

grigsbyanthony/IW-CGA

A comparative genomic analysis of several Ignatzschineriaceae spp.

Language: R - Size: 3.71 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

linas/biome-distribution

Research into statistical distributions of genomes, proteomes and reactomes

Language: Scheme - Size: 14.2 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 0

Appsilon/shiny.gosling

R Shiny wrapper for Gosling.js - Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization

Language: R - Size: 13.7 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 18 - Forks: 1

RCollins13/HumanIdiogramLibrary

Resource of human chromosome schematics & images

Size: 21.1 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 84 - Forks: 11

lebinary/genome-browser

Genome browser to visualize and analyze genomic data

Language: JavaScript - Size: 2.37 MB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 13 - Forks: 2

epiviz/epiviz.gl

Visualize genomic data using webgl and webworkers, in an effort to provide a fluid, high-performance user experience.

Language: JavaScript - Size: 68.1 MB - Last synced at: 28 days ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 5

Zhenglabhku/WormSynteny

Visualize the synteny or genomic conservation among eleven nematode Caenorhabditis species.

Language: R - Size: 87.1 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

kpatel427/R-scripts

Miscellaneous R script to wrangle data and generate visualizations

Language: R - Size: 146 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 15 - Forks: 10

johnvusich/johnvusich.github.io

My personal website

Language: HTML - Size: 1.35 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

Ahmedyassin300/Mendelian-Genetics-Algorithm

Mendelian Genetics Algorithm

Language: Python - Size: 4.88 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

solislemuslab/bioklustering

BioKlustering: a web app for semi-supervised learning of maximally unbalanced genomic data

Language: Jupyter Notebook - Size: 42.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 3

G3viz/g3lollipop.js

Lollipop-diagram to visualize genomic mutations

Language: JavaScript - Size: 10.8 MB - Last synced at: 11 months ago - Pushed at: almost 6 years ago - Stars: 19 - Forks: 13

vaishnavipaithane/Genomic-Data-and-Management-Analysis

This miniproject is part of 'Fundamentals of Python Programming' virtual internship conducted by Nyberman Bioinformatics, Europe.

Language: Python - Size: 22.5 KB - Last synced at: 3 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

brentp/seqcover

seqcover allows users to view coverage for hundreds of genes and dozens of samples

Language: Nim - Size: 9.45 MB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 50 - Forks: 4

euxhenh/cellar

Interactive software tool for the assignment of cell types in single-cell studies.

Language: Python - Size: 51.9 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 31 - Forks: 7

sscansan/genomics_and_GWAS_tutorials

Analysis of SNP variants, derived from chip array genotyping and HTS sequencing

Language: HTML - Size: 26.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

YogiOnBioinformatics/Maternal-to-Zygotic-Transition-in-Xenopus-laevis

Research project undertaken in Computational Genomics at the University of Pittsburgh. with Dr. Miler Lee and students to understand Maternal-to-Zygotic transition in Xenopus laevis

Language: Shell - Size: 1.9 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

brwnj/covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

Language: HTML - Size: 126 MB - Last synced at: 27 days ago - Pushed at: over 3 years ago - Stars: 56 - Forks: 7

s1monj/nft-peppers

Generative Art NFTs from Genomic Data

Language: JavaScript - Size: 118 MB - Last synced at: 4 days ago - Pushed at: over 3 years ago - Stars: 20 - Forks: 8

jslfree080/bamscope

A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)

Language: Java - Size: 207 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 0

ovsama/Genomic_Data_Science

Here is a whole bunch of genomic data analyses using Bioconductor packages. The files are found in the form of .R files.

Language: R - Size: 178 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine

Genomic Interactive Visualization Engine

Language: JavaScript - Size: 72 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 140 - Forks: 32

LyonsLab/coge

CoGe (Comparative Genomics) Platform

Language: Perl - Size: 162 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 44 - Forks: 17

cmdoret/tinycov

Command line tool to plot genomic coverage from a BAM file

Language: Python - Size: 34.8 MB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 13 - Forks: 5

MaryAgopian/Variant_Barcoding_M.orygis

Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.

Language: R - Size: 55.7 KB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

nlawlor/Multiomic_Browser

An R shiny application for visualization of EndoC-bH1 and human islet genomic data

Language: R - Size: 18 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

c3g/epivar-browser

Source code for the EpiVar browser, a web application to search for eQTL/epigenetic signal-associated variants and merge bigWig tracks by genotype.

Language: JavaScript - Size: 39.5 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

biojs/biojs-frontend 📦

Frontend repository for BioJS.

Language: Vue - Size: 3.35 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 12

fllstx/kaplan-meier-estimator

Kaplan-Meier-Estimator also known as the product limit estimator.

Language: TypeScript - Size: 707 KB - Last synced at: 29 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

NAL-i5K/genomics-workspace

Django website project for common sequence search tools.

Language: JavaScript - Size: 444 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 5

eblancoga/seqcode

Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data

Language: C - Size: 4.26 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 12 - Forks: 2

snesic/manhattan-plot-eQTLs-per-gene

Language: R - Size: 4.58 MB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 2

mindleaving/genome-tools

Tools for exploration and analysis of biochemical data like genomics and proteins

Language: C# - Size: 905 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 2

ikergarcia1996/Gene2Tab

This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.

Language: Python - Size: 28.3 KB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

LankyCyril/edgecase

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Language: Python - Size: 167 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 2

colindaven/jbrowse2_utils

Bash scripts for writing assemblies and tracks to JBrowse2 https://jbrowse.org/jb2/

Language: Shell - Size: 18.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

The1stMartian/GCskewAnalyzer

Analyzes the GC skew of bacterial chromosomes using multiple calculations. Outputs a data frame of GC skew values and wiggle files for visualization.

Language: Python - Size: 2.39 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

amcrisan/GEVitRec

Visualization recommender and UI for complex non-tabular data and linked static charts

Language: HTML - Size: 5.5 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 2

ManinderpreetPuri/Artificial-Intelligence-In-Bioinfromatics-Project1

Computer Science and Information Technology Professionals are being employed in many diverse areas of Science. In this project are focusing on Bioinformatics and the knowledge and skills to understand and participate in this field of research or as an advance step to greater employment opportunities. This project will clarify the fundamentals of Bioinformatics from the end user perspective and will allow us to participate in information gathering.

Size: 1.78 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1