diff --git a/DESCRIPTION b/DESCRIPTION index 0d76f70..a6e3dc8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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 diff --git a/NEWS.md b/NEWS.md index 84af76f..212812f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# methylTFRAnnotationMm10 0.99.7 +# methylTFRAnnotationMm10 0.99.9 * Initial submission to Bioconductor. diff --git a/inst/extdata/metadata.csv b/inst/extdata/metadata.csv index 392fe44..27cbc8d 100644 --- a/inst/extdata/metadata.csv +++ b/inst/extdata/metadata.csv @@ -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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","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 ","GRangesList","Rds","https://zenodo.org/","records/22207136/files/jaspar2020_tf_bindsites.rds","methylTFRAnnotationMm10:TFBS:MotifAnnotation:JASPAR2020" diff --git a/inst/scripts/make-metadata.R b/inst/scripts/make-metadata.R index b0b8509..eb478f3 100644 --- a/inst/scripts/make-metadata.R +++ b/inst/scripts/make-metadata.R @@ -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( @@ -56,15 +56,15 @@ meta <- data.frame( Maintainer = "Irem B. Gunduz ", 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", @@ -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!") } \ No newline at end of file