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| methylMnM-package | MeDIP-Seq and MRE-Seq data analysis |
| calcFactornew | Normalization factor. |
| calculatecount | Call C programs to R. |
| calculatecount1 | Call C programs to R. |
| calculatecountneg | Call C programs to R. |
| CNVnormal | Normalize copy number variation (CNV). |
| countcpgbin | Compute the total CpG number of each bin with each CpG site. |
| countMeDIPbin | Compute the total MeDIP-seq number of each bin. |
| countMREbin | Compute the total MRE-seq number of each bin. |
| countMREcpgbin | Compute the MRE CpG number of each bin with MRE CpG sites. |
| cpgcount | Call C programs to R. |
| methylMnM | MeDIP-Seq and MRE-Seq data analysis |
| MnM.qvalue | Estimate the q-values for a given set of p-values |
| MnM.selectDMR | Select significants of each comparation. |
| MnM.test | Compute p-value of each bin. |
| normpdf | Compute p-value with normal distribution. |
| normpdft1 | Compute p-value with normal distribution. |
| pmultinom | Call C programs to R. |
| qvalue.rank | Rank values. |
| removeblacklist | Remove blacklist. |