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PeakSegDisk (version 2022.2.1)

Disk-Based Constrained Change-Point Detection

Description

Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).

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Install

install.packages('PeakSegDisk')

Monthly Downloads

671

Version

2022.2.1

License

GPL-3

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Maintainer

Toby Hocking

Last Published

February 2nd, 2022

Functions in PeakSegDisk (2022.2.1)

ChIPreads

Reads aligned to hg19 from two ChIP-seq experiments
PeakSegFPOP_df

PeakSeg penalized solver for data.frame
summary.PeakSegFPOP_dir

summary PeakSegFPOP dir
wc2int

wc2int
Mono27ac

A small ChIP-seq data set in which peaks can be found using PeakSegFPOP
plot.PeakSegFPOP_dir

plot PeakSegFPOP dir
PeakSegFPOP_dir

PeakSeg penalized solver with caching
sequentialSearch_dir

Compute PeakSeg model with given number of peaks
col.name.list

col name list
fread.first

Quickly read first line
PeakSegFPOP_file

PeakSegFPOP using disk storage
PeakSegFPOP_vec

PeakSeg penalized solver for integer vector
writeBedGraph

Write bedGraph file
coef.PeakSegFPOP_dir

coef PeakSegFPOP dir
coef.PeakSegFPOP_df

coef PeakSegFPOP df
fread.last

Quickly read last line
plot.PeakSegFPOP_df

plot PeakSegFPOP df