YuLab-SMU/DOSE

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YuLab-SMU/DOSE

YuLab-SMU

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😷 Disease Ontology Semantic and Enrichment analysis

DOSE: Disease Ontology Semantic and Enrichment analysis

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

For details, please visit https://yulab-smu.top/biomedical-knowledge-mining-book/.

✍️ Authors

Guangchuang YU https://yulab-smu.top

School of Basic Medical Sciences, Southern Medical University

Please cite the following article when using DOSE:

G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.

clusterProfiler

📊 A universal enrichment tool for interpreting omics data

ggtree

🎄Visualization and annotation of phylogenetic trees

enrichplot

Visualization of Functional Enrichment Result

ChIPseeker

🎯 ChIP peak Annotation, Comparison and Visualization

ggmsa

🚥 Visualizing publication-quality multiple sequence alignment using ggplot2

MicrobiotaProcess

🦠 A comprehensive R package for deep mining microbiome

ggbreak

💔 An implementation of scale functions for setting axis breaks of a 'gg' plot.

treedata-book

📚 a complete reference book for treeio, tidytree and ggtree packages

aplot

Decorate a plot with associated information

treeio

🌱 Base Classes and Functions for Phylogenetic Tree Input and Output

ggtreeExtra

🍋 Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”

biomedical-knowledge-mining-book

📚 Biomedical knowledge mining using GOSemSim and clusterProfiler

scatterpie

🎨 scatter pie plot

createKEGGdb

Create KEGG.db Package

GOSemSim

⛳ GO-terms Semantic Similarity Measures

plotbb

🖌️ Grammar of Graphics for base plot

tidytree

🚿A Tidy Tool for Phylogenetic Tree Data Manipulation

fanyi

Translate Words or Sentences via Online Translators

ggsc

🧠 Visualizing Single Cell and Spatial Transcriptomics

ReactomePA

Reactome Pathway Analysis

MicrobiomeProfiler

🦠 A shiny package for microbiome functional enrichment analysis

ProjectYulab

⏭️ Small coding tasks that enable you to participate in our development

yulab.utils

Miscellaneous functions commonly used by 'YuLab-SMU'.

treedataverse

Meta package for processing and visualizing tree with data

plotting-tree-with-data-using-ggtreeExtra

tigeR

🐯 tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package

GeoTcgaData

Processed rna-seq data, copy number variation data, and methylation data on GEO and TCGA

seqcombo

Visualization tool for genetic reassortment

nCov2019

🦠 Exploring COVID-19 data

ggfun

useful functions for ggplot

wget

download files in R using wget -c

survival-guide

YuLab的生存秘笈

clusterProfiler.dplyr

dplyr verbs for clusterProfiler outputs

TDbook

A Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees"

tidydr

MMINP

Microbe-Metabolite INteractions-based metabolic profiles Predictor

clusterProfiler-book

a complete reference book for clusterProfiler and its sub-packages

ggtreeDendro

Drawing 'dendrogram' using 'ggtree'

yulab-smu.github.io

🏠 Homepage for YuLab-SMU

meshes

🩺 MeSH Enrichment and Semantic analyses

clusterProfiler_protocol

omics data analysis using clusterProfiler ;)

MicrobiotaProcessWorkshop

The workshop of microbiome datasets analysis using MicrobiotaProcess

shinyTempSignal

Explore Temporal and Other Phylogenetic Signals

ggflow

Draw flow chart based on ggtree

mirrorselect

To help select CRAN and Bioconductor mirrors.

aplotExtra

Creating composite plot using 'aplot'

rdpvis

Visualizing sequence break point

sc2p

single cell to pathway

iggtree

interactive tree viewer using ggtree + shiny

learnggtree

Tutorial for Learning 'ggtree'

seqmagick

sequence manipulation

supplemental-clusterProfiler-v4

ggtreeSpace

🕸️Exploring phylomorphospace using 'ggtree'

wikiprofiler

supplemental-ggbreak

SVP

msacolor

HDO.db

A new version of DO.db

simpleGO

Simple GO Enrichment Analysis

BMplot

Base Modification Visualization

MP_supplementary_file

ggcircos

misc

ggmsaBioWorkshop2021

multiEnrichment

multi-omic enrichment analysis

ggtangle

Draw Network with Data

gson

lab_dot_files

sclet

MPO.db

mh_analysis

ChIPseeker_current_protocols

gson-files

ggacmap

plotting acmap using ggplot2

HPO.db

COSemSim

An R package measures semantic similarity value for cell types, genes and proteins

supplemental-ggmsa