Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary
Repository
plots function for array
Basic Info
- Host: GitHub
- Owner: xjsun1221
- License: other
- Language: R
- Default Branch: master
- Size: 35.1 MB
Statistics
- Stars: 94
- Watchers: 2
- Forks: 27
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
tinyarray
Introduction
Hi, I'm Xiao Jie. This is an R package I wrote based on my own data analysis needs. I'm glad you found it. I will update some useful functions here on the public account "bioinfoplanet" and also do some other sharing.
Installation
1.online
if(!require(tinyarray))install.packages("tinyarray")
if(!require(devtools))install.packages("devtools")
if(!require(tinyarray))devtools::install_github("xjsun1221/tinyarray",upgrade = FALSE,dependencies = TRUE)
2.local
Click the green button "code" on this page, then click "Download ZIP" to download it to your working directory. Install it with devtools::install_local("tinyarray-master.zip",upgrade = F,dependencies = T).
functions
1.basic
drawheatmap(),drawvolcano(),drawvenn(),drawboxplot(),drawKM(),drawvenn(),risk_plot()
ggheat() is a function from the ggplot2 package that can be used to create heatmaps. It is still relatively immature and mainly used for aligning plots and collecting legends.
Something about ggheat(): https://mp.weixin.qq.com/s/WhsBf6QAhVXeXeScM59cSA
2.Downstream Analysis of Gene Expression Array Data from GEO Database
geo_download(): Provide a GEO number and get back the expression matrix, clinical information table, and platform number used.
find_anno(): Look up the annotation of the array platform.
get_deg(): Provide the array expression matrix, grouping information, probe annotation and get back the differential analysis results.
multi_deg(): Differential analysis for multiple groups (up to 5).
If you want to do differential analysis and get the common figures in one step, you can use getdegall() and multidegall(). This part mainly integrates and simplifies the differential analysis of GEOquery, Annoprobe, and limma.
quick_enrich(): Simple and intuitive enrichment analysis.
double_enrich(): Separate enrichment of up- and down-regulated genes, combined with plotting.
https://mp.weixin.qq.com/s/YQQoDsE5JaKpgFGlbEfQNg
https://mp.weixin.qq.com/s/j5IBMQ0zeOCe1jahwtdQ
3.Exploring Expression Matrices
maketcgagroup(): Quickly get the grouping according to the TCGA sample naming rules.
sam_filter(): Remove duplicate tumor samples in TCGA.
matchexpcl(): Match TCGA expression matrix with clinical information.
trans_array(): Replace the row names of the matrix, such as replacing the probe names of the expression matrix with gene names.
trans_exp(): Convert TCGA or TCGA+GTeX data to gene IDs (old version, genecode v22 or v23)
transexpnew(): Convert TCGA or TCGA+GTeX data to gene IDs(new versions)
t_choose(): Do t-tests for individual genes in batches.
cor.full() and cor.one(): Calculate correlations between genes in batches.
4.Survival Analysis and Visualization
point_cut(): Calculate the best cutoff point for survival analysis in batches.
surv_KM(): Do KM survival analysis in batches, supporting grouping with the best cutoff point.
surv_cox(): Do single factor Cox in batches, supporting grouping with the best cutoff point.
risk_plot(): Risk factor three-way linkage.
https://mp.weixin.qq.com/s/WYBhGxfGg6QFUPHFBashaA
exp_boxplot(): Draw T-N boxplot for the interested genes.
exp_surv(): Draw KM-plot for the interested genes.
box_surv(): Draw boxplot and KM-plot for the interested genes.
5.Something about network graph
hypertest(): Do hypergeometric distribution test for mRNA and lncRNA in batches.
plcortest(): Do correlation test for mRNA and lncRNA in batches.
https://www.yuque.com/xiaojiewanglezenmofenshen/bsgk2d/dt0isp
interactiontoedges(): Generate the connection table for the network graph based on the relationship table.
edgestonodes(): Generate the node table based on the connection table.
6.Tricks
dumd(): Count how many values each column of the data frame has.
intersect_all(): Take the intersection of any number of vectors.
union_all(): Take the union of any number of vectors.
Owner
- Name: Xiaojie Sun
- Login: xjsun1221
- Kind: user
- Location: Zhuhai, Guangdong Province
- Repositories: 3
- Profile: https://github.com/xjsun1221
instructor of biotrainee（WeChat public account） Co-founder of bioinfoplanet（WeChat public account） author in jianshu.com
GitHub Events
Total
- Issues event: 2
- Watch event: 9
- Issue comment event: 1
- Pull request event: 1
- Fork event: 3
Last Year
- Issues event: 2
- Watch event: 9
- Issue comment event: 1
- Pull request event: 1
- Fork event: 3
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| xjsun1221 | x****1@1****m | 102 |
| Bioinfoplanet | B****0@o****m | 54 |
| Xiaojie Sun | 5****1 | 8 |
| 小洁 | k****e@b****l | 7 |
| Bioinfoplanet | b****0@o****m | 4 |
| xjsun1221 | x****e@X****l | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 11
- Total pull requests: 1
- Average time to close issues: 6 months
- Average time to close pull requests: N/A
- Total issue authors: 11
- Total pull request authors: 1
- Average comments per issue: 1.73
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: 5 months
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kaifenghuang07 (1)
- Dabaixian (1)
- seasonzhao (1)
- Kevinhokahey (1)
- quaresma00 (1)
- huangshenghao666 (1)
- swcyo (1)
- julin06 (1)
- ydx1013 (1)
- zhangyz1997 (1)
- ayueme (1)
- hjames1 (1)
Pull Request Authors
- kusurin (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 1,175 last-month
- Total docker downloads: 21,613
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 10
- Total maintainers: 1
cran.r-project.org: tinyarray
Expression Data Analysis and Visualization
- Homepage: https://github.com/xjsun1221/tinyarray
- Documentation: http://cran.r-project.org/web/packages/tinyarray/tinyarray.pdf
- License: MIT + file LICENSE
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Latest release: 2.4.3
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5.0 depends
- BiocManager * imports
- clusterProfiler * imports
- dplyr * imports
- ggplot2 * imports
- limma * imports
- magrittr * imports
- org.Hs.eg.db * imports
- patchwork * imports
- pheatmap * imports
- stringr * imports
- survival * imports
- survminer * imports
- tibble * imports
- AnnoProbe * suggests
- Biobase * suggests
- ComplexHeatmap * suggests
- FactoMineR * suggests
- GEOquery * suggests
- Rtsne * suggests
- VennDiagram * suggests
- circlize * suggests
- cowplot * suggests
- factoextra * suggests
- ggplotify * suggests
- ggpubr * suggests
- knitr * suggests
- labeling * suggests
- rmarkdown * suggests
- scatterplot3d * suggests
- testthat * suggests
- tidyr * suggests