Datasets: Internal raw datasets.

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

Internal raw datasets in BED6 format. All genome positions where converted to the most recent genome assembly version; i.e. for human data, all positions are given in GRCh38/hg38 coordinates. For mouse data, positions are given in mm10 coordinates.

Details

bsRNAseq_m5C_Squires2012_hg38.bed

bsRNA-seq 5-methylcytosine (m5C) sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/22344696

HITSCLIP_eIF4A3_Sauliere2012_hg38.bed

HITSCLIP eIF4AIII binding sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/23085716

MeRIPseq_m1A_Dominissini2016_hg38.bed

MeRIP-seq N(1)-methyladenosine (m1A) sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/26863196

miCLIP_m6A_Linder2015_hg38.bed

miCLIP N(6)-methyladenosine (m6A) sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/26121403

PARCLIP_AGO1234_Hafner2010_hg38.bed

PAR-CLIP AGO1-4 binding sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/20371350

PARCLIP_eIF3_Meyer2015_hg38.bed

PAR-CLIP eIF3 binding sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/26593424

PARCLIP_eIF3_Lee2015_hg38.bed

PAR-CLIP eIF3 binding sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/25849773

PARCLIP_YTHDF2_Wang2014_hg38.bed

PAR-CLIP YTHDF2 binding sites. Reference: https://www.ncbi.nlm.nih.gov/pubmed/24284625

PseudoU_Schwartz2014_Li2015_hg38.bed

Merged Psi-seq and CeU-seq pseudouridine (Psi) sites. References: https://www.ncbi.nlm.nih.gov/pubmed/25219674, https://www.ncbi.nlm.nih.gov/pubmed/26075521

TargetScan_miRNAtargets_hg38.bed

TargetScan-based miRNA target sites. Reference: http://www.targetscan.org/vert_72/

Author(s)

Maurits Evers, [e-mail]

Examples

## Not run: 
bedFile <- ReadBED(system.file(
    "extdata",
    "miCLIP_m6A_Linder2015_hg38.bed",
    package = "RNAModR")

## End(Not run)

mevers/RNAModR documentation built on Nov. 17, 2019, 9:11 a.m.