| Title: | data package for xcore |
|---|---|
| Description: | Provides data to use with xcore package. |
| Authors: | Maciej Migdał [aut, cre] (ORCID: <https://orcid.org/0000-0002-8021-7263>), Bogumił Kaczkowski [aut] (ORCID: <https://orcid.org/0000-0001-6554-5608>) |
| Maintainer: | Maciej Migdał <[email protected]> |
| License: | GPL-2 |
| Version: | 1.17.0 |
| Built: | 2026-10-10 10:45:27 UTC |
| Source: | https://github.com/bioc/xcoredata |
Metadata associated with chip_atlas_promoters.
chip_atlas_metachip_atlas_meta
A data.frame with 13891 rows and 5 columns.
Character giving internal experiment ID.
Character giving transcription factor name.
Character giving transcription factor DNA binding domain family, as per CIS BP database.
Character giving experiment biological origin.
Character giving study ID.
chip_atlas_meta()chip_atlas_meta()
An intersection matrix describing overlaps between ChIP-Atlas's ChIP-seq tracks
and promoters_f5. To find overlapping regions promoters were extended
by 500bp in both directions.
chip_atlas_promoters_f5chip_atlas_promoters_f5
A Matrix with 209911 rows and 13891 columns. Row names corresponds to promoters
names, column names are formatted as TranscriptionFactor_Origin_Cell_ExperimentID
(eg. PARK7_Neural_SH-SY5Y_DRX000550, MLL-AF6_Blood_ML-2_DRX001460).
chip_atlas_promoters_f5()chip_atlas_promoters_f5()
Vector mapping ENTREZ IDs to FANTOM5 core promoters names.
entrez2fantomentrez2fantom
A named character vector of length 14214.
entrez2fantom()entrez2fantom()
FANTOM5's hg38 promoters annotated with nearest features in GENCODE ver. 38 annotation and UCSC hg38 knownGene annotation ver. 3.13.0.
promoters_f5promoters_f5
A GenomicRanges object of length 209911, with 11 metadata columns:
Promotor name.
Numeric vector.
Gene type of associated gene as defined by GENCODE annotation.
ENTREZ ID of associated gene as defined by all three annotation sources. Prevalence of annotations: UCSC > GENCODE > FANTOM5.
Gene symbol of associated gene as defined by all three annotation sources. Prevalence of annotations: UCSC > GENCODE > FANTOM5.
promoters_f5()promoters_f5()
Core promoters selected from promoters_f5. Selection criteria were GENCODE confirmation and ENCODE ROADMAP confirmation. Further for each gene single promoter with highest FANTOM5 score was selected.
promoters_f5_corepromoters_f5_core
A GenomicRanges object of length 14191, with 16 metadata columns:
Promotor name.
Numeric vector.
Gene type of associated gene as defined by GENCODE annotation.
ENTREZ ID of associated gene as defined by all three annotation sources. Prevalence of annotations: UCSC > GENCODE > FANTOM5.
Gene symbol of associated gene as defined by all three annotation sources. Prevalence of annotations: UCSC > GENCODE > FANTOM5.
promoters_f5_core()promoters_f5_core()
Metadata associated with remap_promoters.
remap_metaremap_meta
A data.table with 5798 rows and 6 columns.
Character giving internal experiment ID.
Character giving transcription factor name.
Character giving transcription factor DNA binding domain family, as per CIS BP database.
Character giving experiment biological origin.
Character giving study ID.
Character specifiying experiment conditions or treatment.
remap_meta()remap_meta()
An intersection matrix describing overlaps between ReMap2020's ChIP-seq tracks
and promoters_f5. To find overlapping regions promoters were extended
by 500bp in both directions.
remap_promoters_f5remap_promoters_f5
A Matrix with 209911 rows and 5728 columns. Row names corresponds to promoters names, column names are formatted as ExperimentID.TranscriptionFactor.Biotype.
remap_promoters_f5()remap_promoters_f5()
Vector mapping gene symbols to FANTOM5 core promoters names.
symbol2fantomsymbol2fantom
A named character vector of length 14222.
symbol2fantom()symbol2fantom()