Software

Hi-C
- HiCRep: Measure reproducibility of Hi-C contact matrices. download
- OnTAD: A Optimal Nested TAD caller to identify hierarchical TADs from Hi-C data. download
Assessing reproducibility of high-throughput experiments
- IDR: Assessing reproducibility of ranked candidate lists from high-throughput experiments. This method has been adoped by ENCODE to process their production ChIP-seq data download. Here is the link to ENCODE ChIP-seq pipeline.
- gIDR: Generalized irreproducible discover rate for assessing reproducibility of findings from high-throughput experiments when missing data is present.
  download
- mTDR: Tail-dependence method for assessing reproducibility of ChIP-seq experiments. download
- nestedIDR: A nested copula mixture model to identify reproducible findings from replicates that come from heterogeneous data sources. download
Use reproducibility to guide the experimental design of high-throughput experiments
- CCR: Evaluate effects of operational factors to reproducibility of findings from high-throughput experiments and help users select optimal experimental parameter. download
- segCCR: Evaluate effects of operational factors to reproducibility of findings from high-throughput experiments, when the effects are heterogeneous for findings at different level of significance. download
Data integration across platforms for gene expression data
- CFGL: Condition-adaptive graphical lasso for constructing gene co-expression networks from multiple conditions. download
- idr3c: A semi-parametric statistical model for integrating gene expression profiles across different platforms. download
Immunology
- powerTCR: discrete Gamma-GPD spliced threshold model for analysis of TCR repertoire sequencing data.
  download
Segmented regression
- cthreshER: Fit the continuous threshold expectile regression. download
- Rbent: Fit rank-based bent line regression. download