Software
- space (Sparse PArtial
Correlation Estimation): space is an R package for estimation and
identification of non-zero partial correlations via sparse regression techniques.
It can be downloaded from http://cran.r-project.org/; or by clicking space. It is useful in construction of large networks.
For more details, see the paper: Peng, Wang, Zhou and Zhu (2009).
Partial Correlation Estimation by Joint Sparse Regression Models, Journal
of the American Statistical Association, Vol. 104, No. 486, 735-746 [technical report: pdf; arXiv:0811.4463]
- fpca (Functional Principal Component
Analysis): fpca is an R package for estimation eigen-values and eigen-functions
of the convariance kernel (fpca)
via sparsely observed functional data. It can be downloaded from
http://cran.r-project.org/; or by clicking fpca. It is useful
in longitudinal studies. For more details, see the paper: Peng and Paul
(2009). A geometric approach to maximum likelihood estimation of the
functional principal components from sparse longitudinal data, Journal of
Computational and Graphical Statistics, 18(4): 995 - 1015 [pdf]
(technical report: arXiv:0710.5343v1);
1-29-09: updated R package fpca
- remMap (REgularized Multivariate regression for identifying MAster Predictors): remMap
is an R package for fitting multivariate regression models under
high-dimension-low-sample-size setting. It can be downloaded from http://cran.r-project.org/; or by clicking remMap. It is useful
in construction of networks by using two types of high dimensional data,
e.g., CGH array and expression array. For more details, see the paper: Peng, Zhu, Bergamaschi,
Han, Noh, Pollack and Wang (2010) Regularized Multivariate Regression for
Identifying Master Predictors with Application to Integrative Genomics
Study of Breast Cancer, The Annals of Applied Statistics, 4 (1): 53-77 [technical report: pdf; arXiv:0812.3671v1].
- dynamics:
dynamics is an R package for fitting autonomous dynamical systems using
spline basis (B-splines or cubic polynomial splines). It can be downloaded
by clicking dynamics. dynamics is useful for fitting the
underlying common (autonomous) systems nonparametrically
for a group of random curves when only a snapshot of each sample curve is
observed. For more details, see the paper: Paul, Peng and Burman (2011) Semiparametric
modeling of autonomous nonlinear dynamical systems with applications, The Annals of Applied Statistics, 5(3): 2078-2108 [technical report: pdf,
arXiv:0906.3501v1]
- BINCO (Bootstrap Inference for Network COnstruction): BINCO
is an R package to calculate the optimal threshold of selection
frequencies for variable/feature selection through directly controlling
the false discovery rate. It can be downloaded from http://cran.r-project.org/.
It
is useful for determining the amount of regularization in high-dimension
regularization problems, particularly, unsupervised learning such as
network structure learning. For more details, see the paper
: Li, Hsu, Peng and Wang (2013). Bootstrap
inference for network construction, The Annals of Applied
Statistics, 7(1): 391-417. [Full Text].
- dagbag: dagbag is an R package to conduct DAG learning
by hill climbing algorithm and bootstrap aggregating. It can be downloaded from
https://github.com/jie108/dagbag.
dagbag
is useful for high-dimensional directed acyclic graph (DAG) model
learning. For more details, see the paper: R. Wang and J. Peng.
Learning directed acyclic graphs via bootstrap aggregating (2014). [arXiv:1406.2098]
- spaceMap: spaceMap is an
integrative –omics analysis pipeline for constructing
networks and conducting network analysis. It is maintained on https://topherconley.github.io/spacemap/. spaceMap is useful for high-dimensional
conditional graphical model learning. For more details, see the paper: Conley C., Umut Ozbek, Wang P., and J. Peng. Characterizing functional consequences of DNA copy
number alterations in breast and ovarian tumors
by spaceMap (2018). Journal of Genetics and
Genomics, 45(7): 361–371.
[bioRxiv: 10.1101/248229]
- PLNet (Poisson Lognormal Network): PLNet is an R package to infer
graphical models and build networks based on RNA-Seq
data. It can be downloaded from https://github.com/jie108/PLNet/. For more details, see the paper: Choi Y., Coram M., J. Peng, and Tang H. A Poisson Log-Normal model for
constructing gene covariation network using RNA-seq data (2017).
Journal of Computational Biology, 24(7): 721-731. [pdf]
- TSNet (Tumor Specific Network):
TSNet
is an R package for constructing tumor-specific networks based on samples
with tumor purity heterogeneity. It can be downloaded from https://github.com/jie108/TSNet.
For more details, see the paper: Francesca Petralia,
Li Wang, J. Peng, Arthur Yan,
Jun Zhu, and Pei Wang. A new method for constructing tumor specific gene
co-expression networks based on samples with tumor purity heterogeneity.
Bioinformatics, 34(13): i528–i536, 2018.
[html]
- loggle (LOcal Group Graphical Lasso Estimation): loggle is an R package for constructing time-varying
graphical models. It can be downloaded from http://cran.r-project.org/.
For more details, see the paper: Jilei Yang and J.
Peng. Estimating time-varying graphical models (2018). [arxiv:804.03811].