Package 'RNAmodR.Data'

RNAmodR example data for tests and man pages

Description

This dataset contains a small data set for tests and man page examples. The indivicual identifiers are RNAmodR.Data. plus the header from the Datasets section.

Datasets

example.man.fasta

sequence of artificial genome for S. cerevisiae containing partial sequences of the 18S rRNA

example.man.gff3

annotation of artificial genome for S. cerevisiae containing partial sequences of the 18S rRNA

Examples

RNAmodR.Data.example.man.fasta()
RNAmodR.Data.example.man.gff3()

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RNAmodR.Data

Description

RNAmodR.Data contains example data, which is used for vignettes and example workflows in the RNAmodR and dependent packages.

Author(s)

Felix G.M. Ernst [aut], Denis L.J. Lafontaine [ctb]

See Also

Useful links:

• https://github.com/FelixErnst/RNAmodR.Data

• Report bugs at https://github.com/FelixErnst/RNAmodR.Data/issues

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RNAmodR AlkAnilineSeq example data

Description

This dataset contains exmaple data for AlkAnilineSeq. The indivicual identifiers are RNAmodR.Data. plus the header from the Datasets section.

Datasets

example.AAS.fasta

sequence of artificial genome for S. cerevisiae containing only the 18S rRNA sequence and 10 tRNA sequences

example.AAS.gff3

annotation of artificial genome for S. cerevisiae containing only the 18S rRNA sequence and 10 tRNA sequences

example.bud23.1

sequencing reads mapped to artificial genome from bud23del strain - replicate 1

example.bud23.2

sequencing reads mapped to artificial genome from bud23del strain - replicate 2

example.trm8.1

sequencing reads mapped to artificial genome from trm8del strain - replicate 1

example.trm8.2

sequencing reads mapped to artificial genome from trm8del strain - replicate 2

example.wt.1

sequencing reads mapped to artificial genome from wild type strain - replicate 1

example.wt.2

sequencing reads mapped to artificial genome from wild type strain - replicate 2

example.wt.3

sequencing reads mapped to artificial genome from wild type strain - replicate 3

Examples

RNAmodR.Data.example.AAS.fasta()
RNAmodR.Data.example.AAS.gff3()
RNAmodR.Data.example.bud23.1()
RNAmodR.Data.example.bud23.2()
RNAmodR.Data.example.trm8.1()
RNAmodR.Data.example.trm8.2()
RNAmodR.Data.example.wt.1()
RNAmodR.Data.example.wt.2()
RNAmodR.Data.example.wt.3()

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RNAmodR general example data

Description

This dataset contains general example data used for different purposes. The indivicual identifiers are RNAmodR.Data. plus the header from the Datasets section.

Datasets

example.fasta

sequences of artificial genome for S. cerevisiae containing only rRNA and tRNA sequences

example.gff3

annotation of artificial genome for S. cerevisiae containing only rRNA and tRNA sequences

example.bam.1

sequencing reads mapped to artificial genome - replicate 1

example.bam.2

sequencing reads mapped to artificial genome - replicate 2

example.bam.3

sequencing reads mapped to artificial genome - replicate 3

Examples

RNAmodR.Data.example.fasta()
RNAmodR.Data.example.gff3()
RNAmodR.Data.example.bam.1()
RNAmodR.Data.example.bam.2()
RNAmodR.Data.example.bam.3()

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RNAmodR RiboMethSeq example data

Description

This dataset contains example data for RiboMethSeq. The indivicual identifiers are RNAmodR.Data. plus the header from the Datasets section.

Datasets

example.RMS.fasta

sequence of artificial genome for H. sapiens containing only the 5.8S rRNA sequence

example.RMS.gff3

annotation of artificial genome for H. sapiens containing only the 5.8S rRNA sequence

example.RMS.1

sequencing reads mapped to artificial genome - replicate 1

example.RMS.2

sequencing reads mapped to artificial genome - replicate 2

Examples

RNAmodR.Data.example.RMS.fasta()
RNAmodR.Data.example.RMS.gff3()
RNAmodR.Data.example.RMS.1()
RNAmodR.Data.example.RMS.2()

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snoRNAdb data

Description

The csv files contains a copy of data from the snoRNAdb (https://www-snorna.biotoul.fr/) downloaded on the 2019-02-11. The coordinates were updated to current rRNA sequences of hg38.

Examples

RNAmodR.Data.snoRNAdb()

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