ChIPtest: Nonparametric Methods for Identifying Differential Enrichment Regions with ChIP-Seq Data

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Nonparametric Tests to identify the differential enrichment region for two conditions or time-course ChIP-seq data. It includes: data preprocessing function, estimation of a small constant used in hypothesis testing, a kernel-based two sample nonparametric test, two assumption-free two sample nonparametric test.

Author
Vicky Qian Wu ; Kyoung-Jae Won ; Hongzhe Li <hongzhe@upenn.edu>
Date of publication
2016-07-20 17:59:16
Maintainer
Vicky Qian Wu <wuqian7@gmail.com>
License
GPL (>= 2.15.1)
Version
1.0

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Man pages

ChIPtest-package
Nonparametric Methods for Identifying Differential Enrichment...
data1
Input data (matrix) for condition A
data4
Input data (matrix) for condition B
est.c
calculate the biologically relevant value c in the null...
NormTransformation
Variance-stabilizing transformation (VST) procedure
TS_kernel
Calculate the Test Statistics for kernel-based nonparametric...
TS_twosample
Three Nonparametric Test Statistics for two sample ChIP-seq...

Files in this package

ChIPtest
ChIPtest/src
ChIPtest/src/ChIPtest_main.cc
ChIPtest/src/ChIPtest.cc
ChIPtest/src/ChIPtest.h
ChIPtest/NAMESPACE
ChIPtest/data
ChIPtest/data/data1.rda
ChIPtest/data/data4.rda
ChIPtest/R
ChIPtest/R/NormTransformation.R
ChIPtest/R/TS_kernel.R
ChIPtest/R/TS_twosample.R
ChIPtest/R/est.c.R
ChIPtest/MD5
ChIPtest/DESCRIPTION
ChIPtest/man
ChIPtest/man/NormTransformation.Rd
ChIPtest/man/data4.Rd
ChIPtest/man/ChIPtest-package.Rd
ChIPtest/man/est.c.Rd
ChIPtest/man/TS_twosample.Rd
ChIPtest/man/TS_kernel.Rd
ChIPtest/man/data1.Rd