Package 'marinerData'

Title: ExperimentHub data for the mariner package
Description: Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). These files are used for testing mariner functions and some examples.
Authors: Eric Davis [aut, cre] (ORCID: <https://orcid.org/0000-0003-4051-3217>)
Maintainer: Eric Davis <[email protected]>
License: GPL-3
Version: 1.12.0
Built: 2026-10-10 11:22:13 UTC
Source: https://github.com/bioc/marinerData

Help Index

Example NHA9 (FS) Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from HEK cells expressing an NHA9 fusion with an F to S mutated IDR.

Value

Downloads and caches a .txt file in BEDPE format.

Examples

bedpeFile <- FS_5kbLoops.txt()
bedpeFile

Example NHA9 (FS) Hi-C data

Description

Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR.

Value

Downloads and caches a .hic file.

Examples

hicFile <- LEUK_HEK_PJA27_inter_30.hic()
hicFile

Example NHA9 (WT) Hi-C data

Description

Subsampled Hi-C in HEK cells expressing the NHA9 fusion with a Wildtype IDR.

Value

Downloads and caches a .hic file.

Examples

hicFile <- LEUK_HEK_PJA30_inter_30.hic()
hicFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 0 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0000.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 30 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0030.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 60 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0060.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 90 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0090.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 120 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0120.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 240 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0240.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 360 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_0360.bedpe()
bedpeFile

Example Timecourse Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from THP-1 cells exposed to LPS & IF-G for 1440 minutes.

Value

Downloads and caches a .bedpe file in BEDPE format.

Examples

bedpeFile <- LIMA_1440.bedpe()
bedpeFile

ExperimentHub datasets for the mariner package

Description

Subsampled Hi-C in HEK cells expressing the NHA9 fusion with an F to S mutated IDR ("FS") or without any mutations to the IDR ("Wildtype" or "WT"). Accompanying loop calls identified using SIP (https://github.com/PouletAxel/SIP) are also provided. For more information or full datasets, see https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143465.

Also included are loop calls identified using SIP (https://github.com/PouletAxel/SIP) from a THP-1 activation timecourse after stimulation with LPS & IF-G for 0, 30, 60, 80, 120, 2440, 360, or 1440 minutes. For more information or full datasets, see https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201353.

These files are used for testing mariner functions and some examples.

Value

Downloads and caches .hic or BEDPE-formatted .txt files.

Author(s)

Eric S. Davis

Example NHA9 (WT) Loops

Description

Loops called with SIP (https://github.com/PouletAxel/SIP) using Hi-C data from HEK cells expressing an NHA9 fusion with a Wildtype IDR.

Value

Downloads and caches a .txt file in BEDPE format.

Examples

bedpeFile <- WT_5kbLoops.txt()
bedpeFile