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Merged
igunduz merged 2 commits into from
Sep 2, 2026
Merged

update metadata #5

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2b59697
update metadata
igunduz Aug 31, 2026
557a011
update biocversion in metadata
igunduz Sep 2, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -15,7 +15,7 @@ Authors@R: person(
comment = c(ORCID = "0000-0003-2641-0916"))
License: Artistic-2.0
Encoding: UTF-8
Version: 0.99.7
Version: 0.99.9
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 @@
# methylTFRAnnotationMm10 0.99.7
# methylTFRAnnotationMm10 0.99.9

* Initial submission to Bioconductor.

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14 changes: 7 additions & 7 deletions inst/extdata/metadata.csv
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@@ -1,8 +1,8 @@
"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 mm10. 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","mm10","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Mus musculus",10090,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/altius_motif_gcfreq.rds","methylTFRAnnotationMm10:GCcontent:MotifAnnotation:ALTIUS"
"altius_tf_bindsites.rds","Genome-wide ALTIUS transcription factor binding site predictions for mm10, 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","mm10","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Mus musculus",10090,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/altius_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:ALTIUS"
"cisbpv2_motif_gcfreq.rds","GC bin frequency tables for CISBPV2 motifs on mm10. 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","mm10","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Mus musculus",10090,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/cisbpv2_motif_gcfreq.rds","methylTFRAnnotationMm10:GCcontent:MotifAnnotation:CISBPV2"
"cisbpv2_tf_bindsites.rds","Genome-wide CISBPV2 transcription factor binding site predictions for mm10, 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","mm10","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Mus musculus",10090,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/cisbpv2_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:CISBPV2"
"genomewide_GC_mm10.rds","Genome-wide GC content distribution for mm10. 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","mm10","RDS","https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/","mm10","Mus musculus",10090,TRUE,"UCSC","Irem B. Gunduz <irembgunduz@gmail.com>","GRanges","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/genomewide_GC_mm10.rds","methylTFRAnnotationMm10:GCcontent:Genome"
"jaspar2020_motif_gcfreq.rds","GC bin frequency tables for JASPAR2020 motifs on mm10. 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","mm10","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Mus musculus",10090,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/jaspar2020_motif_gcfreq.rds","methylTFRAnnotationMm10:GCcontent:MotifAnnotation:JASPAR2020"
"jaspar2020_tf_bindsites.rds","Genome-wide JASPAR2020 transcription factor binding site predictions for mm10, 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","mm10","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Mus musculus",10090,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://bioconductorhubs.blob.core.windows.net/annotationhub/","methylTFRAnnotationMm10/jaspar2020_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:JASPAR2020"
"altius_motif_gcfreq.rds","GC bin frequency tables for ALTIUS motifs on mm10. 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","mm10","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Mus musculus",10090,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22207136/files/altius_motif_gcfreq.rds","methylTFRAnnotationMm10:GCcontent:MotifAnnotation:ALTIUS"
"altius_tf_bindsites.rds","Genome-wide ALTIUS transcription factor binding site predictions for mm10, 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","mm10","RDS","https://resources.altius.org/~jvierstra/projects/motif-clustering/releases/v1.0/","Vierstra motif archetypes v1.0","Mus musculus",10090,TRUE,"Altius Institute","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://zenodo.org/","records/22207136/files/altius_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:ALTIUS"
"cisbpv2_motif_gcfreq.rds","GC bin frequency tables for CISBPV2 motifs on mm10. 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","mm10","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Mus musculus",10090,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22207136/files/cisbpv2_motif_gcfreq.rds","methylTFRAnnotationMm10:GCcontent:MotifAnnotation:CISBPV2"
"cisbpv2_tf_bindsites.rds","Genome-wide CISBPV2 transcription factor binding site predictions for mm10, 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","mm10","RDS","https://github.com/GreenleafLab/chromVARmotifs","CIS-BP v2 (chromVARmotifs pwms_v2)","Mus musculus",10090,TRUE,"CIS-BP","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://zenodo.org/","records/22207136/files/cisbpv2_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:CISBPV2"
"genomewide_GC_mm10.rds","Genome-wide GC content distribution for mm10. 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","mm10","RDS","https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/","mm10","Mus musculus",10090,TRUE,"UCSC","Irem B. Gunduz <irembgunduz@gmail.com>","GRanges","Rds","https://zenodo.org/","records/22207136/files/genomewide_GC_mm10.rds","methylTFRAnnotationMm10:GCcontent:Genome"
"jaspar2020_motif_gcfreq.rds","GC bin frequency tables for JASPAR2020 motifs on mm10. 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","mm10","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Mus musculus",10090,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","list","Rds","https://zenodo.org/","records/22207136/files/jaspar2020_motif_gcfreq.rds","methylTFRAnnotationMm10:GCcontent:MotifAnnotation:JASPAR2020"
"jaspar2020_tf_bindsites.rds","Genome-wide JASPAR2020 transcription factor binding site predictions for mm10, 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","mm10","RDS","https://jaspar.elixir.no/","JASPAR2020 CORE","Mus musculus",10090,TRUE,"JASPAR","Irem B. Gunduz <irembgunduz@gmail.com>","GRangesList","Rds","https://zenodo.org/","records/22207136/files/jaspar2020_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:JASPAR2020"
20 changes: 10 additions & 10 deletions inst/scripts/make-metadata.R
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Expand Up @@ -20,7 +20,7 @@ meta <- data.frame(
"GC bin frequency tables for JASPAR2020 motifs on mm10. 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 mm10, 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 = "3.23",
BiocVersion = "3.24",
Genome = "mm10",
SourceType = "RDS",
SourceUrl = c(
Expand Down Expand Up @@ -56,15 +56,15 @@ meta <- data.frame(
Maintainer = "Irem B. Gunduz <irembgunduz@gmail.com>",
RDataClass = c("list", "GRangesList", "list", "GRangesList", "GRanges", "list", "GRangesList"),
DispatchClass = "Rds",
Location_Prefix = "https://bioconductorhubs.blob.core.windows.net/annotationhub/",
Location_Prefix = "https://zenodo.org/",
RDataPath = c(
"methylTFRAnnotationMm10/altius_motif_gcfreq.rds",
"methylTFRAnnotationMm10/altius_tf_bindsites.rds",
"methylTFRAnnotationMm10/cisbpv2_motif_gcfreq.rds",
"methylTFRAnnotationMm10/cisbpv2_tf_bindsites.rds",
"methylTFRAnnotationMm10/genomewide_GC_mm10.rds",
"methylTFRAnnotationMm10/jaspar2020_motif_gcfreq.rds",
"methylTFRAnnotationMm10/jaspar2020_tf_bindsites.rds"
"records/22207136/files/altius_motif_gcfreq.rds",
"records/22207136/files/altius_tf_bindsites.rds",
"records/22207136/files/cisbpv2_motif_gcfreq.rds",
"records/22207136/files/cisbpv2_tf_bindsites.rds",
"records/22207136/files/genomewide_GC_mm10.rds",
"records/22207136/files/jaspar2020_motif_gcfreq.rds",
"records/22207136/files/jaspar2020_tf_bindsites.rds"
),
Tags = c(
"methylTFRAnnotationMm10:GCcontent:MotifAnnotation:ALTIUS",
Expand All @@ -85,6 +85,6 @@ write.csv(meta, file = "inst/extdata/metadata.csv", row.names = FALSE)
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!")
}