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igunduz merged 2 commits into from
Sep 2, 2026
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update metadata #3

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035900d
update metadata
igunduz Aug 31, 2026
a58a5a2
update biocversion in metadata
igunduz Sep 2, 2026
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12 changes: 7 additions & 5 deletions DESCRIPTION
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Expand Up @@ -9,13 +9,15 @@ Description: Precomputed transcription factor binding sites, motif GC
for sequence composition. The data are hosted on AnnotationHub and
retrieved on first use; this package provides the accessors and the
documentation.
Authors@R: person(
given = "Irem B.", family = "Gunduz",
email = "irembgunduz@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-2641-0916"))
Authors@R: c(
person("Irem B.", "Gündüz", , "irembgunduz@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-2641-0916")),
person("Fabian", "Muller", , "fabian.mueller@uni-saarland.de", role = "aut",
comment = c(ORCID = "0000-0001-5809-2321"))
)
License: Artistic-2.0
Encoding: UTF-8
Version: 0.99.6
Version: 0.99.8
Depends: R (>= 4.3.0)
Imports: AnnotationHub, GenomicRanges, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
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2 changes: 1 addition & 1 deletion NEWS.md
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@@ -1,4 +1,4 @@
# methylTFRAnnotationHg38 0.99.6
# methylTFRAnnotationHg38 0.99.8

* Initial submission to Bioconductor.

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16 changes: 8 additions & 8 deletions inst/extdata/metadata.csv
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@@ -1,9 +1,9 @@
"Title","Description","BiocVersion","Genome","SourceType","SourceUrl","SourceVersion","Species","TaxonomyId","Coordinate_1_based","DataProvider","Maintainer","RDataClass","DispatchClass","Location_Prefix","RDataPath","Tags"
"altius_motif_gcfreq.rds","GC bin frequency tables for ALTIUS motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.23","hg38","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Homo sapiens",9606,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/altius_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:ALTIUS"
"altius_tf_bindsites.rds","Genome-wide ALTIUS transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.","3.23","hg38","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Homo sapiens",9606,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/altius_tf_bindsites.rds","methylTFRAnnotationHg38:TFBS:MotifAnnotation:ALTIUS"
"cisbpv2_motif_gcfreq.rds","GC bin frequency tables for CISBPV2 motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.23","hg38","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Homo sapiens",9606,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/cisbpv2_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:CISBPV2"
"cisbpv2_tf_bindsites.rds","Genome-wide CISBPV2 transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.","3.23","hg38","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Homo sapiens",9606,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/cisbpv2_tf_bindsites.rds","methylTFRAnnotationHg38:TFBS:MotifAnnotation:CISBPV2"
"genomewide_GC_hg38.rds","Genome-wide GC content distribution for hg38. A GRanges of tiled windows carrying GC_bias and a GC_bin assignment into genome-wide quintiles. methylTFR uses it to assign each methylation call to a GC bin.","3.23","hg38","RDS","https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/","hg38","Homo sapiens",9606,TRUE,"UCSC","Irem B. Gunduz <irembgunduz@gmail.com>","GRanges","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/genomewide_GC_hg38.rds","methylTFRAnnotationHg38:GCcontent:Genome"
"jaspar2020_distal_motif_gcfreq.rds","GC bin frequency tables for JASPAR2020_DISTAL motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.23","hg38","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Homo sapiens",9606,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/jaspar2020_distal_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:JASPAR2020_DISTAL"
"jaspar2020_motif_gcfreq.rds","GC bin frequency tables for JASPAR2020 motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.23","hg38","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Homo sapiens",9606,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/jaspar2020_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:JASPAR2020"
"jaspar2020_tf_bindsites.rds","Genome-wide JASPAR2020 transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.","3.23","hg38","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Homo sapiens",9606,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationHg38/jaspar2020_tf_bindsites.rds","methylTFRAnnotationHg38:TFBS:MotifAnnotation:JASPAR2020"
"altius_motif_gcfreq.rds","GC bin frequency tables for ALTIUS motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.24","hg38","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Homo sapiens",9606,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22206980/files/altius_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:ALTIUS"
"altius_tf_bindsites.rds","Genome-wide ALTIUS transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.","3.24","hg38","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Homo sapiens",9606,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://zenodo.org/","records/22206980/files/altius_tf_bindsites.rds","methylTFRAnnotationHg38:TFBS:MotifAnnotation:ALTIUS"
"cisbpv2_motif_gcfreq.rds","GC bin frequency tables for CISBPV2 motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.24","hg38","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Homo sapiens",9606,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22206980/files/cisbpv2_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:CISBPV2"
"cisbpv2_tf_bindsites.rds","Genome-wide CISBPV2 transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.","3.24","hg38","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Homo sapiens",9606,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://zenodo.org/","records/22206980/files/cisbpv2_tf_bindsites.rds","methylTFRAnnotationHg38:TFBS:MotifAnnotation:CISBPV2"
"genomewide_GC_hg38.rds","Genome-wide GC content distribution for hg38. A GRanges of tiled windows carrying GC_bias and a GC_bin assignment into genome-wide quintiles. methylTFR uses it to assign each methylation call to a GC bin.","3.24","hg38","RDS","https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/","hg38","Homo sapiens",9606,TRUE,"UCSC","Irem B. Gunduz <irembgunduz@gmail.com>","GRanges","Rds","https://zenodo.org/","records/22206980/files/genomewide_GC_hg38.rds","methylTFRAnnotationHg38:GCcontent:Genome"
"jaspar2020_distal_motif_gcfreq.rds","GC bin frequency tables for JASPAR2020_DISTAL motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.24","hg38","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Homo sapiens",9606,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22206980/files/jaspar2020_distal_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:JASPAR2020_DISTAL"
"jaspar2020_motif_gcfreq.rds","GC bin frequency tables for JASPAR2020 motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.","3.24","hg38","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Homo sapiens",9606,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22206980/files/jaspar2020_motif_gcfreq.rds","methylTFRAnnotationHg38:GCcontent:MotifAnnotation:JASPAR2020"
"jaspar2020_tf_bindsites.rds","Genome-wide JASPAR2020 transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.","3.24","hg38","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Homo sapiens",9606,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://zenodo.org/","records/22206980/files/jaspar2020_tf_bindsites.rds","methylTFRAnnotationHg38:TFBS:MotifAnnotation:JASPAR2020"
52 changes: 26 additions & 26 deletions inst/scripts/make-metadata.R
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@@ -1,13 +1,13 @@
# 1. Define the shared (constant) variables for cleaner code
bioc_version <- "3.23"
bioc_version <- "3.24"
genome <- "hg38"
source_type <- "RDS"
species <- "Homo sapiens"
tax_id <- 9606
coord_1_based <- TRUE
maintainer <- "Irem B. Gunduz <irembgunduz@gmail.com>"
dispatch_class <- "Rds"
location_prefix <- "https://bioconductorhubs.blob.core.windows.net/annotationhub/"
location_prefix <- "https://zenodo.org/"

# 2. Build the data frame
metadata <- data.frame(
Expand All @@ -21,7 +21,7 @@ metadata <- data.frame(
"jaspar2020_motif_gcfreq.rds",
"jaspar2020_tf_bindsites.rds"
),

Description = c(
"GC bin frequency tables for ALTIUS motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.",
"Genome-wide ALTIUS transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window.",
Expand All @@ -32,11 +32,11 @@ metadata <- data.frame(
"GC bin frequency tables for JASPAR2020 motifs on hg38. One five-row matrix per motif giving the number of binding sites falling in each genome-wide GC quintile, used by methylTFR to compute the expected methylation a motif would show from GC content alone.",
"Genome-wide JASPAR2020 transcription factor binding site predictions for hg38, one GRanges per motif, each range extended by 200 bases on either side of the motif match so that methylTFR can read methylation across the footprint window."
),

BiocVersion = rep(bioc_version, 8),
Genome = rep(genome, 8),
SourceType = rep(source_type, 8),

SourceUrl = c(
"https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/",
"https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/",
Expand All @@ -47,7 +47,7 @@ metadata <- data.frame(
"https://jaspar.elixir.no/",
"https://jaspar.elixir.no/"
),

SourceVersion = c(
"Vierstra motif archetypes v1.0",
"Vierstra motif archetypes v1.0",
Expand All @@ -58,11 +58,11 @@ metadata <- data.frame(
"JASPAR2020 CORE",
"JASPAR2020 CORE"
),

Species = rep(species, 8),
TaxonomyId = rep(tax_id, 8),
Coordinate_1_based = rep(coord_1_based, 8),

DataProvider = c(
"Altius Institute",
"Altius Institute",
Expand All @@ -73,9 +73,9 @@ metadata <- data.frame(
"JASPAR",
"JASPAR"
),

Maintainer = rep(maintainer, 8),

RDataClass = c(
"list",
"GRangesList",
Expand All @@ -86,21 +86,21 @@ metadata <- data.frame(
"list",
"GRangesList"
),

DispatchClass = rep(dispatch_class, 8),
Location_Prefix = rep(location_prefix, 8),

RDataPath = c(
"methylTFRAnnotationHg38/altius_motif_gcfreq.rds",
"methylTFRAnnotationHg38/altius_tf_bindsites.rds",
"methylTFRAnnotationHg38/cisbpv2_motif_gcfreq.rds",
"methylTFRAnnotationHg38/cisbpv2_tf_bindsites.rds",
"methylTFRAnnotationHg38/genomewide_GC_hg38.rds",
"methylTFRAnnotationHg38/jaspar2020_distal_motif_gcfreq.rds",
"methylTFRAnnotationHg38/jaspar2020_motif_gcfreq.rds",
"methylTFRAnnotationHg38/jaspar2020_tf_bindsites.rds"
"records/22206980/files/altius_motif_gcfreq.rds",
"records/22206980/files/altius_tf_bindsites.rds",
"records/22206980/files/cisbpv2_motif_gcfreq.rds",
"records/22206980/files/cisbpv2_tf_bindsites.rds",
"records/22206980/files/genomewide_GC_hg38.rds",
"records/22206980/files/jaspar2020_distal_motif_gcfreq.rds",
"records/22206980/files/jaspar2020_motif_gcfreq.rds",
"records/22206980/files/jaspar2020_tf_bindsites.rds"
),

Tags = c(
"methylTFRAnnotationHg38:GCcontent:MotifAnnotation:ALTIUS",
"methylTFRAnnotationHg38:TFBS:MotifAnnotation:ALTIUS",
Expand All @@ -111,7 +111,7 @@ metadata <- data.frame(
"methylTFRAnnotationHg38:GCcontent:MotifAnnotation:JASPAR2020",
"methylTFRAnnotationHg38:TFBS:MotifAnnotation:JASPAR2020"
),

stringsAsFactors = FALSE
)

Expand All @@ -120,16 +120,16 @@ metadata <- data.frame(
dir.create("inst/extdata", recursive = TRUE, showWarnings = FALSE)

write.csv(
x = metadata,
file = "inst/extdata/metadata.csv",
row.names = FALSE,
x = metadata,
file = "inst/extdata/metadata.csv",
row.names = FALSE,
quote = TRUE # This ensures strings containing spaces/commas are properly enclosed
)

# Validate using AnnotationHubData
if (!requireNamespace("AnnotationHubData", quietly = TRUE)) {
message("Please install AnnotationHubData to validate your metadata.csv")
} else {
AnnotationHubData::makeAnnotationHubMetadata("inst/extdata")
AnnotationHubData::makeAnnotationHubMetadata(".")
message("Metadata validation completed successfully!")
}