"BiocVersion","Genome","SourceVersion","Coordinate_1_based","Maintainer","Title","Description","SourceType","DataProvider","RDataClass","DispatchClass","RDataPath","Species","TaxonomyId","SourceUrl"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.fasta","rRNA and tRNA sequences from S. cerevisiae. rRNA sequences from SGD and tRNA sequences retrieved from tRNAscan-SE output were used. tRNA sequences with Levensthein distances >= 3 were kept. This is used as anartificial genome for example data.","FASTA","SGD, tRNAscan-SE","FaFile","FaFile","RNAmodR.Data/example.fasta:RNAmodR.Data/example.fai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.gff3","Artificial annotations for rRNA and tRNA sequences from S. cerevisiae. rRNA sequences from SGD and tRNA sequences retrieved from tRNAscan-SE output were used. tRNA sequences with Levensthein distances >= 3 were kept. This is used as an artificial genome for example data.","GFF","SGD, tRNAscan-SE","FilePath","FilePath","RNAmodR.Data/example.gff3","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.bam.1","Mapped reads to artificial genome. Reads were taken from sequencing results from AlkAnilineSeq project (DOI: 10.1002/anie.201810946). Replicate 1","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example1.bam:RNAmodR.Data/example1.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.bam.2","Mapped reads to artificial genome. Reads were taken from sequencing results from AlkAnilineSeq project (DOI: 10.1002/anie.201810946). Replicate 2","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example2.bam:RNAmodR.Data/example2.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.bam.3","Mapped reads to artificial genome. Reads were taken from sequencing results from AlkAnilineSeq project (DOI: 10.1002/anie.201810946). Replicate 3","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example3.bam:RNAmodR.Data/example3.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.RMS.fasta","5.8S rRNA sequence from H. sapiens.","FASTA","SGD, tRNAscan-SE","FaFile","FaFile","RNAmodR.Data/example_RMS.fasta:RNAmodR.Data/example_RMS.fai","Homo sapiens","9606","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.RMS.gff3","Artificial annotation for 5.8S rRNA sequence from H. sapiens.","GFF","SGD, tRNAscan-SE","FilePath","FilePath","RNAmodR.Data/example_RMS.gff3","Homo sapiens","9606","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.RMS.1","Mapped reads to 5.8S rRNA of H. sapiens. Reads were taken from sequencing results from RiboMethSeq project (DOI: tbd). Replicate 1","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_RMS1.bam:RNAmodR.Data/example_RMS1.bai","Homo sapiens","9606","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.RMS.2","Mapped reads to 5.8S rRNA of H. sapiens. Reads were taken from sequencing results from RiboMethSeq project (DOI: tbd). Replicate 2","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_RMS2.bam:RNAmodR.Data/example_RMS2.bai","Homo sapiens","9606","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.AAS.fasta","18S rRNA and 10 tRNA sequences from S. cerevisiae. rRNA sequence from SGD and tRNA sequences retrieved from tRNAscan-SE output were used. 10 tRNA were selected manually. This is used as an artificial genome for example data and sequences are named chr1-chr11.","FASTA","SGD, tRNAscan-SE","FaFile","FaFile","RNAmodR.Data/example_AAS.fasta:RNAmodR.Data/example_AAS.fai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.AAS.gff3","Annotations for 18S rRNA and 10 tRNA sequences from S. cerevisiae. rRNA sequence from SGD and tRNA sequences retrieved from tRNAscan-SE output were used. 10 tRNA were selected manually. This is used for an artificial genome for example data and annotation is for sequences named chr1-chr11.","GFF","SGD, tRNAscan-SE","FilePath","FilePath","RNAmodR.Data/example_AAS.gff3","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.bud23.1","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for bud23del strain (DOI: 10.1002/anie.201810946). Replicate 1","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_bud23_1.bam:RNAmodR.Data/example_bud23_1.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.bud23.2","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for bud23del strain (DOI: 10.1002/anie.201810946). Replicate 2","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_bud23_2.bam:RNAmodR.Data/example_bud23_2.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.trm8.1","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for trm8del strain (DOI: 10.1002/anie.201810946). Replicate 1","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_trm8_1.bam:RNAmodR.Data/example_trm8_1.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.trm8.2","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for trm8del strain (DOI: 10.1002/anie.201810946). Replicate 2","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_trm8_2.bam:RNAmodR.Data/example_trm8_2.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.wt.1","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for wild type strain (DOI: 10.1002/anie.201810946). Replicate 1","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_wt_1.bam:RNAmodR.Data/example_wt_1.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.wt.2","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for wild type strain (DOI: 10.1002/anie.201810946). Replicate 2","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_wt_2.bam:RNAmodR.Data/example_wt_2.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.wt.3","Mapped reads to 18S rRNA and 10 tRNA of S. cerevisiae. Reads were taken from sequencing results from AlkAnilineSeq project for wild type strain (DOI: 10.1002/anie.201810946). Replicate 3","FASTQ","UMS2008 Next Generation Sequencing (NGS) Core Facility, Lorraine University","BamFile","BamFile","RNAmodR.Data/example_wt_3.bam:RNAmodR.Data/example_wt_3.bai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.man.fasta","Nucleotides at position 1-100 and 1500-1600 of 18S rRNA from S. cerevisiae.","FASTA","SGD, tRNAscan-SE","FaFile","FaFile","RNAmodR.Data/example1.fasta:RNAmodR.Data/example1.fai","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,NA,TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.example.man.gff3","Annotations for nucleotides at position 1-100 and 1500-1600 of 18S rRNA from S. cerevisiae.","GFF","SGD, tRNAscan-SE","FilePath","FilePath","RNAmodR.Data/example1.gff3","Saccharomyces cerevisiae S288C","559292","http://www.lafontainelab.com"
"3.9",NA,"2019-02-11",TRUE,"Felix G.M. Ernst <felix.gm.ernst@outlook.com>","RNAmodR.Data.snoRNAdb","Information from the snoRNAdb was downloaded and manually adjusted for changes in recent rRNA sequences from H. sapiens. The information provided match hg38 release sequences.","TXT","snoRNAdb","FilePath","FilePath","RNAmodR.Data/snoRNAdb.csv","Homo sapiens","9606","https://www-snorna.biotoul.fr/"
