Topic: "genomics-visualization"
moshi4/pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Language: Python - Size: 57.3 MB - Last synced at: 8 days ago - Pushed at: 3 months ago - Stars: 859 - Forks: 50
thackl/gggenomes
A grammar of graphics for comparative genomics
Language: R - Size: 111 MB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 661 - Forks: 65
moshi4/pyGenomeViz
A genome visualization python package for comparative genomics
Language: Python - Size: 76.2 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 319 - Forks: 21
bernatgel/karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Language: R - Size: 3.06 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 307 - Forks: 41
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: 3 days ago - Pushed at: 4 months ago - Stars: 283 - Forks: 113
ucscGenomeBrowser/kent
UCSC Genome Browser source tree. Stable branch: "beta".
Language: C - Size: 564 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 234 - Forks: 92
mixOmicsTeam/mixOmics
Development repository for the Bioconductor package 'mixOmics '
Language: R - Size: 16.9 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 191 - Forks: 60
stevekm/IGV-snapshot-automator
Script to automatically create and run IGV snapshot batchscripts
Language: Python - Size: 26.4 MB - Last synced at: 16 days ago - Pushed at: over 2 years ago - Stars: 140 - Forks: 50
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
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: about 1 month ago - Pushed at: almost 2 years ago - Stars: 126 - Forks: 7
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
CDCgov/MicrobeTrace Fork of AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: TypeScript - Size: 140 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 92 - Forks: 41
robotoD/GenoVi
GenoVi, an automated customizable circular genome visualizer for bacteria and archaea
Language: Python - Size: 175 MB - Last synced at: 24 days ago - Pushed at: almost 2 years ago - Stars: 89 - Forks: 11
RCollins13/HumanIdiogramLibrary
Resource of human chromosome schematics & images
Size: 21.1 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 84 - Forks: 11
arvkevi/ezancestry
Easy genetic ancestry predictions in Python
Language: Jupyter Notebook - Size: 24.9 MB - Last synced at: 21 days ago - Pushed at: about 2 months ago - Stars: 65 - Forks: 11
thierrygosselin/radiator
RADseq Data Exploration, Manipulation and Visualization using R
Language: HTML - Size: 11 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 59 - Forks: 23
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: 10 days ago - Pushed at: about 3 years ago - Stars: 56 - Forks: 7
daler/trackhub
create, manage, and upload track hubs for use in the UCSC genome browser
Language: Python - Size: 13.3 MB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 53 - Forks: 20
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: about 1 month ago - Pushed at: about 4 years ago - Stars: 50 - Forks: 4
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
moshi4/MGCplotter 📦
Microbial Genome Circular plotting tool for comparative genomics using Circos
Language: Python - Size: 68.1 MB - Last synced at: 2 days ago - Pushed at: about 2 years ago - Stars: 38 - Forks: 7
tobiasrausch/vc
A tutorial on structural variant calling for short read sequencing data
Language: R - Size: 111 KB - Last synced at: 8 days ago - Pushed at: 6 months ago - Stars: 32 - Forks: 2
euxhenh/cellar
Interactive software tool for the assignment of cell types in single-cell studies.
Language: Python - Size: 51.9 MB - Last synced at: 10 months ago - Pushed at: about 2 years ago - Stars: 31 - Forks: 7
gtrichard/deepStats
deepStats: a stastitical toolbox for deeptools and genomic signals
Language: R - Size: 8.53 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 30 - Forks: 3
thierrygosselin/stackr
stackr: an R package to run stacks software pipeline
Language: HTML - Size: 20.9 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 29 - Forks: 8
hw538/cfDNAPro
cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis
Language: R - Size: 2.94 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 29 - Forks: 3
G3viz/g3viz
Lollipop-diagram to interactively visualize genetic mutations
Language: JavaScript - Size: 65.2 MB - Last synced at: 5 months ago - Pushed at: 7 months ago - Stars: 29 - Forks: 19
PacificBiosciences/SVTopo
Complex structural variant visualization for HiFi sequencing data
Language: HTML - Size: 115 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 26 - Forks: 2
nf-core/hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
Language: Nextflow - Size: 5.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 24 - Forks: 6
GMOD/jbrowse-jupyter
A python package for showing JBrowse views
Language: Python - Size: 6.45 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 24 - Forks: 4
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: 4 days ago - Pushed at: almost 3 years ago - Stars: 20 - Forks: 4
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
czheluo/Circos-Pipeline
circos pipeline
Language: Perl - Size: 37.7 MB - Last synced at: 20 days ago - Pushed at: almost 4 years ago - Stars: 20 - Forks: 14
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: 11 days ago - Pushed at: almost 2 years ago - Stars: 19 - Forks: 3
G3viz/g3lollipop.js
Lollipop-diagram to visualize genomic mutations
Language: JavaScript - Size: 10.8 MB - Last synced at: 10 months ago - Pushed at: over 5 years ago - Stars: 19 - Forks: 13
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: 5 months ago - Pushed at: 11 months ago - Stars: 18 - Forks: 1
outbreak-info/R-outbreak-info
R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.
Language: R - Size: 91.1 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 17 - Forks: 9
hoffmangroup/segway
Application for semi-automated genomic annotation.
Language: Shell - Size: 31 MB - Last synced at: 8 days ago - Pushed at: 9 months ago - Stars: 16 - Forks: 7
kdyrhage/GenomicMaps.jl
Julia package for visualising genomic data
Language: Julia - Size: 2.5 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 2
w-gao/pgv
A web-based, interactive pangenome visualization tool
Language: TypeScript - Size: 1.15 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 16 - Forks: 0
moshi4/plot_genome_align_fig 📦
Plot genome alignment figure using progressiveMauve & genoPlotR
Language: Python - Size: 37 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4
kpatel427/R-scripts
Miscellaneous R script to wrangle data and generate visualizations
Language: R - Size: 146 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 15 - Forks: 10
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: about 1 month ago - Pushed at: 11 months ago - Stars: 15 - Forks: 3
biojs/biojs-frontend 📦
Frontend repository for BioJS.
Language: Vue - Size: 3.35 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 15 - Forks: 12
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: about 1 year ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 2
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
Binomica-Labs/BLSS
A suite of unique bioinformatics tools for the brave explorer.
Language: C# - Size: 229 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 14 - Forks: 1
cmdoret/tinycov
Command line tool to plot genomic coverage from a BAM file
Language: Python - Size: 34.8 MB - Last synced at: 11 days ago - Pushed at: about 2 years ago - Stars: 13 - Forks: 5
lebinary/genome-browser
Genome browser to visualize and analyze genomic data
Language: JavaScript - Size: 2.37 MB - Last synced at: about 4 hours ago - Pushed at: over 3 years ago - Stars: 13 - Forks: 2
AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Language: HTML - Size: 68.5 MB - Last synced at: 9 days ago - Pushed at: 7 months ago - Stars: 12 - Forks: 42
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: almost 3 years ago - Stars: 12 - 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: 9 days ago - Pushed at: 11 months ago - Stars: 10 - Forks: 5
broadinstitute/gene-hints
Discoverability for gene search :dna: :mag:
Language: Python - Size: 66.2 MB - Last synced at: 9 months ago - Pushed at: about 2 years ago - Stars: 10 - Forks: 0
bernatgel/karyoploter_tutorial
Examples on how to use the karyoploteR R/Bioconductor package
Size: 20.4 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 10 - Forks: 4
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
epiviz/epiviz-desktop-app
Desktop app for epiviz
Language: JavaScript - Size: 14.3 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 10 - Forks: 0
fjdf/slaMEM
Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array
Language: C - Size: 566 KB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 10 - Forks: 5
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
arvkevi/tgviz
1000 Genomes Project population visualizations using dimensionality reduction
Language: Python - Size: 51.9 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 5
neuhausi/canvasxpress-js
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Language: CSS - Size: 36.9 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 8 - Forks: 0
KrasnitzLab/SCGV
SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer
Language: Python - Size: 209 MB - Last synced at: 10 days ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 2
gluesolutions/glue-genes
glue for genomics and transcriptomics
Language: Python - Size: 13.3 MB - Last synced at: 27 days ago - Pushed at: 3 months ago - Stars: 7 - Forks: 2
j-andrews7/OneLinerOmics
One liner analyses and visualizations for bulk RNA-seq and ChIP-seq data
Language: R - Size: 732 KB - Last synced at: 23 days ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 1
thierrygosselin/grur
grur: an R package tailored for RADseq data imputations
Language: R - Size: 7.46 MB - Last synced at: 12 months ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 0
peaselab/mvftools
Language: Python - Size: 846 KB - Last synced at: about 2 months ago - Pushed at: about 2 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: 8 days ago - Pushed at: 2 months ago - Stars: 6 - Forks: 2
bernatgel/CopyNumberPlots
R package to create plots representing copy number data using karyoploteR
Language: R - Size: 2.06 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 2
linas/biome-distribution
Research into statistical distributions of genomes, proteomes and reactomes
Language: Scheme - Size: 14.2 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 6 - Forks: 0
AntoineHo/SAVi
Simple Alignment Viewer
Language: Python - Size: 225 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 0
brentp/bpbio
basepair bio: a single binary with many useful genomics subtools.
Language: Nim - Size: 96.7 KB - Last synced at: about 1 month ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 2
jasonwong-lab/gghic
gghic
Language: R - Size: 40 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 5 - Forks: 0
node/awesome-circos
A curated list of amazingly awesome Circos resources
Size: 5.86 KB - Last synced at: 8 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0
DEIB-GECO/GMQL-WEB
GMQL WEB Interface
Language: JavaScript - Size: 3.53 MB - Last synced at: 11 days ago - Pushed at: over 5 years ago - Stars: 5 - Forks: 3
gosling-lang/gosling-website
Documentation website of Gosling
Language: MDX - Size: 36.5 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 5
Computational-Rare-Disease-Genomics-WHG/VuTR
Web app to visualise the consequences of high-impact 5' UTR Variants
Language: JavaScript - Size: 218 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0
fllstx/kaplan-meier-estimator
Kaplan-Meier-Estimator also known as the product limit estimator.
Language: TypeScript - Size: 707 KB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1
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: almost 2 years ago - Stars: 4 - Forks: 2
brwnj/covdist
simple coverage distribution profile of aligned samples. useful for sequencing center feedback and topoffs.
Language: HTML - Size: 87.9 KB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 1
gowthamv441/Genomics
Final Year Project Repository for correlating the personality trait with the diseases
Language: Python - Size: 208 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 0
AKU-CITRIC-Center-for-Bioinformatics/ncov
Genomic Epidemiology of SARS-CoV-2 in Pakistan
Size: 57.2 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0
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
BenjaminNarhMadey/R-Codes-for-Plant-Breeding-Genetics-Statistics-and-Genomics
This repository serves as a valuable resource for individuals engaged in data exploration, statistical analysis, and research within the domains of plant breeding, genetics, statistics, and genomics. The purpose of this repository is to share a collection of R codes that can be utilized by others for their own data analysis projects
Language: R - Size: 35.2 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0
nriddiford/svBreaks
Analysis and plotting functions for structural variant breakpoint data
Language: R - Size: 7.84 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1
kandarpRJ/epidecodeR
Online version of tool is live
Language: R - Size: 2.31 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 3 - Forks: 0
alexjschiffer/AutoEmma
Automated Efficient Mixed Model Association Studies - R Package
Language: R - Size: 15.1 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0
NickSto/genome-graphic
Generate visualizations of whole genomes or small sequences
Language: Python - Size: 129 KB - Last synced at: over 1 year ago - Pushed at: about 11 years ago - Stars: 3 - Forks: 1
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: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 3
AminMahpour/Wigman
Generate heatmap plots from genomic BigWig data
Language: Python - Size: 678 KB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0
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 1 month ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0
umccr/igv Fork of igvteam/igv
Interactive Genome Viewer with built-in Amazon Web Services support
Language: Java - Size: 408 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
RuzhangZhao/savis
Adaptive Visualization for Single-cell RNA-seq
Language: R - Size: 72.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0
jamesc99/WashU_RepeatBrowser
Interactive Visualization Browser for Transposable Elements (TEs) community
Size: 782 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0
jajokine/Genomics-and-High-Dimensional-Data
MITx - MicroMasters Program on Statistics and Data Science - Data Analysis: Statistical Modeling and Computation in Applications - Second Project
Language: Jupyter Notebook - Size: 1.46 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - 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: 12 months ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1
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
hello-im-aryss/BIS15W2021_DataScienceforBiologists_R
UC Davis: Data Science for Biologists - R markdown
Language: HTML - Size: 160 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0
joycewang914/Genomic_and_Patient_Transfer_Analyasis_of_Resistant_Bacteria
Active surveillance of newly-admitted nursing home patients for colonization of antibiotic-resistant bacteria reveals that multiple lineages have spread across southeast Michigan healthcare networks.
Language: R - Size: 9.58 MB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0
NathanSiemers/FauxFlow
FauxFlow - Analyze Single Cell Genomics Data in a Flow Cytometry Paradigm
Language: R - Size: 90.1 MB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0
alexpreynolds/tabix-service
A nodejs-based service for requests for tabix-indexed genomic data
Language: JavaScript - Size: 124 KB - Last synced at: 11 days ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 4
mb1511/GenomeWeb
Python package to create line drawings of genomic comparison 'webs'/'hive plots'
Language: Python - Size: 6.19 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0
