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| Author | Name | Description | Access | Publication /Citation |
|---|---|---|---|---|
| DDI Predictor | Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network. | https://www.picb.ac.cn/hanlab/DDI | ||
| 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 | ||
| 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
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| 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 | ||
| 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 | ||
| 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 | ||
| 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 | ||
| 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
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| LandSCENT | Landscape Single Cell Entropy, a R-package for the analysis of single-cell RNA-Seq data. | https://github.com/ChenWeiyan/LandSCENT | ||
| AdmixInfer | Infer population histories under the three typical models | https://www.picb.ac.cn/PGG/resource_file/PGG_Web_Soft/AdmixInfer.tar.gz | ||
| iMAAPs | iMAAPs is a powerful tool to estimate multiple-wave population admixed time | https://www.picb.ac.cn/PGG/resource.php | ||
| 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 | ||
| 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 | ||
| 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 | ||
| bsRNA-seq-m5C
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A pipeline used in our bsRNA-seq m5C calling. | https://github.com/YangLab/bsRNA-seq-m5C | ||
| CIRCexplorer
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A combined strategy to identify circular RNAs. | https://github.com/YangLab/CIRCexplorer |
PMID: 25242744
DOI: 10.1016/j.cell.2014.09.001
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| CIRCexplorer2
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The successor of CIRCexplorer. | https://github.com/YangLab/CIRCexplorer2 | ||
| CIRCfinder
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A pipeline to map junction reads for circular intronic RNAs (ciRNAs) | https://github.com/YangLab/CIRCfinder | ||
| CIRCpseudo
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A pipeline to map back-splicing junction sequences for circRNA-derived pseudogenes. | https://github.com/YangLab/CIRCpseudo | ||
| CIRCshapemapper
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A pipeline to analyze the circSHAPE-MaP data. | https://github.com/YangLab/CIRCshapemapper |
PMID: 25242744
DOI: 10.1016/j.cell.2014.09.001
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| CLEAR/CIRCexplorer3
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A computational pipeline for Circular and Linear RNA. | https://github.com/YangLab/CLEAR | ||
| CSI
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A pipeline to quantitate RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns. | https://github.com/YangLab/CSI | ||
| RADAR
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Devised to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets. | https://github.com/YangLab/RADAR | ||
| TERate
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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
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