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Author	Name	Description	Access	Publication /Citation
Han, JD	DDI Predictor	Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network.	https://www.picb.ac.cn/hanlab/DDI	DOI: 10.1371/journal.pcbi.1002998
Han, JD	DM-BN	Deletion Mutant Bayesian Network to the expression profiles of 544 yeast single or double deletion mutants of transcription factors, chromatin remodeling machinery components, protein kinases and phosphatases in S. cerevisiae.	https://www.picb.ac.cn/hanlab/DM_BN.html	PMID: 24039601 PMCID: PMC3764135 DOI: 10.1371/journal.pgen.1003757
Han, JD	iNPS	An improved algorithm for accurate nucleosome positioning from sequencing data.	https://www.picb.ac.cn/hanlab/iNPS.html	PMID: 25233085 DOI: 10.1038/ncomms5909
Han, JD	SeqSpider	The first Bayesian network algorithm that enables learning from tag distributions and combined with a profile clustering method for noise removal, enables ab initio identification of interactions from multiple sources of heterogeneous data.	https://www.picb.ac.cn/hanlab/seqspider.html	PMID: 23318583 PMCID: PMC3587713 DOI: 10.1038/cr.2013.8
Teschendorff, AE	BMIQ	A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.	http://www.picb.ac.cn/compsysg/Software/BMIQ/BMIQ_1.4.R	DOI: 10.1093/bioinformatics/bts680
Teschendorff, AE	ChAMP	The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.	https://bioconductor.org/packages/release/bioc/html/ChAMP.html	DOI: 10.18129/B9.bioc.ChAMP
Teschendorff, AE	DART	An algorithm designed to evaluate the consistency of prior information molecular signatures in independent molecular data. If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.	http://www.bioconductor.org/packages/release/bioc/html/DART.html	DOI: 10.18129/B9.bioc.DART
Teschendorff, AE	ISVA	Independent Surrogate Variable Analysis, an algorithm for feature selection in the presence of potential confounding factors.	https://cran.r-project.org/web/packages/isva/index.html	PMID: 21471010 DOI: 10.1093/bioinformatics/btr171
Teschendorff, AE	LandSCENT	Landscape Single Cell Entropy, a R-package for the analysis of single-cell RNA-Seq data.	https://github.com/ChenWeiyan/LandSCENT	PMID: 31428694 PMCID: PMC6689007 DOI: 10.1038/s42003-019-0554-8
Xu, SH	AdmixInfer	Infer population histories under the three typical models	https://www.picb.ac.cn/PGG/resource_file/PGG_Web_Soft/AdmixInfer.tar.gz	PMID: 26818889 PMCID: PMC4730239 DOI: 10.1038/srep20048
Xu, SH	iMAAPs	iMAAPs is a powerful tool to estimate multiple-wave population admixed time	https://www.picb.ac.cn/PGG/resource.php
Xu, SH	PEAS V1.0	PEAS V1.0: a package for elementary analysis of SNP data	http://www.picb.ac.cn/PGG/resource_file/PGG_Web_Soft/PEAS.zip	DOI: 10.1111/j.1755-0998.2010.02862.x
Xu, SH	SC	SC (Spatial Coalescent simulator) is a computer simulation tool for modeling spatial coalescent with recombination process.	https://www.picb.ac.cn/PGG/resource.php
Xu, SH	WinXPCNVer	WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.	https://www.picb.ac.cn/PGG/resource.php	DOI: 10.1016/j.ajhg.2015.05.005
Yang, L	bsRNA-seq-m5C	A pipeline used in our bsRNA-seq m⁵C calling.	https://github.com/YangLab/bsRNA-seq-m5C	PMID: 32293435 PMCID: PMC7158060 DOI: 10.1186/s12915-020-00769-5
Yang, L	CIRCexplorer	A combined strategy to identify circular RNAs.	https://github.com/YangLab/CIRCexplorer	PMID: 25242744 DOI: 10.1016/j.cell.2014.09.001
Yang, L	CIRCexplorer2	The successor of CIRCexplorer.	https://github.com/YangLab/CIRCexplorer2	PMID: 27365365 PMCID: PMC5052039 DOI: 10.1101/gr.202895.115
Yang, L	CIRCfinder	A pipeline to map junction reads for circular intronic RNAs (ciRNAs)	https://github.com/YangLab/CIRCfinder	PMID: 24035497 DOI: 10.1016/j.molcel.2013.08.017
Yang, L	CIRCpseudo	A pipeline to map back-splicing junction sequences for circRNA-derived pseudogenes.	https://github.com/YangLab/CIRCpseudo	PMID: 27021280 PMCID: PMC4897178 DOI: 10.1038/cr.2016.42
Yang, L	CIRCshapemapper	A pipeline to analyze the circSHAPE-MaP data.	https://github.com/YangLab/CIRCshapemapper	PMID: 31031002 DOI: 10.1016/j.cell.2019.03.046
Yang, L	CLEAR/CIRCexplorer3	A computational pipeline for Circular and Linear RNA.	https://github.com/YangLab/CLEAR	PMID: 31904419 PMCID: PMC7056929 DOI: 10.1016/j.gpb.2019.11.004
Yang, L	CSI	A pipeline to quantitate RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns.	https://github.com/YangLab/CSI	PMID: 27982734 PMCID: PMC5680680 DOI: 10.1080/15476286.2016.1269999
Yang, L	RADAR	Devised to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets.	https://github.com/YangLab/RADAR	PMID: 32492431 DOI: 10.1016/j.celrep.2020.107723
Yang, L	TERate	TERate is a computational to measure transcription elongation rates (TERs) with 4sUDRB-Seq.	https://github.com/YangLab/TERate	PMID: 27068474 DOI: 10.1016/j.celrep.2016.03.058