README.md

In FanqianYin/omicstoolkits: Integrated bioinformatics toolkits for quantitative omics data analysis

omicstoolkits

Integrated bioinformatics toolkits for quantitative omics data analysis

This is an integrated toolkits focusing on data analysis of omics data like transcriptomic, proteomic, metabolic and any other quantitative omics dataset.

Under development...

Main toolkits

Consensus_Cluster_Analysis()

An toolkit for consensus clustering with multi-clustering algorithms.

Currently supported clustering methods:

hc_ward.D, hc_ward.D2, hc_single, hc_complete, hc_average, hc_mcquitty, hc_median, hc_centroid, hc_diana, kmeans, pam, fanny, hkmeans, Mclust, dbscan, con_kmeans, con_pam, con_hc_ward.D2, con_hc_complete, con_hc_average.

Under development

1. Consensus differential expression analysis

2. Network analysis

3. Regression analysis

4. Time serie anaylsis

5. data normalization

6. TBD

Details for future development plans can be viewed at https://github.com/FanqianYin/omicstoolkits/Features_under_developing.Rmd.

Install package

You can install the source package throuhg:

install.packages("devtools")
devtools::install_github("FanqianYin/omicstoolkits")

Or the latest development version:

install.packages("devtools")
devtools::install_github("FanqianYin/omicstoolkits-dev")

Contact

If you encounter any problem, don't hesitate to cantact me: [e-mail] or [e-mail].

Or report bugs at: https://github.com/FanqianYin/omicstoolkits/issues.

Suggestion: If you have any adivce on these tools, please let me know;

Collaboration: If you are interested in integrating these omicstoolkits, welcome to cooperate.

Development history

Under development: Differential expression analysis, data normalization

7/30/2020 Consensus_Cluster_Analysis: an toolkit focus on sample-based subtyping by using consensus clustering result of multi-clustering algorithms.

Version history

Current version: v0.1.2

v0.1.2 10/27/2020

Add methods for QC-based or QC-free data normalization (could be used at metabolomic or proteomic data, or other similar dataset)

v0.1.1 8/2/2020

Consensus_Cluster_Analysis toolkit: Add plot_consensus_clusters.heatmap(), plot_consensus_clusters.pca(), plot_cluster_algorithms.pca(), plot_cluster.pca(), for visulaztion result of Consensus_Cluster_Analysis().

v0.1.0 7/30/2020

Consensus_Cluster_Analysis toolkit: First release.

FanqianYin/omicstoolkits documentation built on Jan. 3, 2022, 5:57 p.m.