FitHiC: Confidence estimation for intra-chromosomal contact maps

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FitHiC")
AuthorFerhat Ay [aut] (Python original, https://noble.gs.washington.edu/proj/fit-hi-c/), Timothy L. Bailey [aut], William S. Noble [aut], Ruyu Tan [aut, cre, trl] (R port)
Bioconductor views DNA3DStructure Software
Date of publicationNone
MaintainerRuyu Tan <rut003@ucsd.edu>
LicenseGPL (>= 2)
Version1.2.0

View on Bioconductor

Functions

FitHiC Man page

Files

DESCRIPTION
NAMESPACE
R
R/FitHiC.R R/RcppExports.R
README.md
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/fithic.R
inst/doc/fithic.Rmd
inst/doc/fithic.html
inst/extdata
inst/extdata/biasPerLocus
inst/extdata/biasPerLocus/Dixon_hESC_HindIII_hg18_w40000_chr1.gz
inst/extdata/biasPerLocus/data_5000000_iced.matrix.biases.gz
inst/extdata/contactCounts
inst/extdata/contactCounts/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz
inst/extdata/contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz
inst/extdata/contactCounts/Dixon_mESC_HindIII_mm9_combineFrags10_chr1.gz
inst/extdata/contactCounts/Duan_yeast_EcoRI.gz
inst/extdata/contactCounts/Duan_yeast_HindIII.gz
inst/extdata/contactCounts/data_5000000.matrix.gz
inst/extdata/fragmentLists
inst/extdata/fragmentLists/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz
inst/extdata/fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz
inst/extdata/fragmentLists/Dixon_mESC_HindIII_mm9_combineFrags10_chr1.gz
inst/extdata/fragmentLists/Duan_yeast_EcoRI.gz
inst/extdata/fragmentLists/Duan_yeast_HindIII.gz
inst/extdata/fragmentLists/data_5000000_abs.bed.gz
man
man/FitHiC.Rd
src
src/FitHiC_init.c
src/RcppExports.cpp
src/helper.cpp
vignettes
vignettes/fithic.Rmd

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