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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
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
Han, JD
iNPS An improved algorithm for accurate nucleosome positioning from sequencing data. https://www.picb.ac.cn/hanlab/iNPS.html
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
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
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
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
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
Teschendorff, AE
LandSCENT Landscape Single Cell Entropy, a R-package for the analysis of single-cell RNA-Seq data. https://github.com/ChenWeiyan/LandSCENT
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
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
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
Yang, L
bsRNA-seq-m5C A pipeline used in our bsRNA-seq m5C calling. https://github.com/YangLab/bsRNA-seq-m5C
Yang, L
CIRCexplorer A combined strategy to identify circular RNAs. https://github.com/YangLab/CIRCexplorer
Yang, L
CIRCexplorer2 The successor of CIRCexplorer. https://github.com/YangLab/CIRCexplorer2
Yang, L
CIRCfinder A pipeline to map junction reads for circular intronic RNAs (ciRNAs) https://github.com/YangLab/CIRCfinder
Yang, L
CIRCpseudo A pipeline to map back-splicing junction sequences for circRNA-derived pseudogenes. https://github.com/YangLab/CIRCpseudo
Yang, L
CIRCshapemapper A pipeline to analyze the circSHAPE-MaP data. https://github.com/YangLab/CIRCshapemapper
Yang, L
CLEAR/CIRCexplorer3 A computational pipeline for Circular and Linear RNA. https://github.com/YangLab/CLEAR
Yang, L
CSI A pipeline to quantitate RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns. https://github.com/YangLab/CSI
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
Yang, L
TERate TERate is a computational to measure transcription elongation rates (TERs) with 4sUDRB-Seq. https://github.com/YangLab/TERate