bioc-issue-bot
commented
11 months ago Hi @mtekman
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: CustomGenome
Type: Package
Title: Append Custom FASTA Sequences to your Genome and Annotation Files for Downstream Mapping
Version: 0.99.0
Authors@R:
c(person(given="Mehmet", family="Tekman",
email = "mtekman89@gmail.com",
role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4181-2676")),
person(given="Sebastian", family="Arnold",
email = "sebastian.arnold@pharmakol.uni-freiburg.de",
role = c("fnd"), comment = c(ORCID = "0000-0002-2688-9210")))
Description: CustomGenome generates a new Ensembl reference genome
sequence and annotation files with custom FASTA sequences (e.g.
GFP, Tomato) and produces RNA-seq count matrices with them. Genome
reference files are fetched and validated directly from Ensembl,
user-sequences are then appended to both, and then the new
reference files are written to disk. Downstream analysis is then
facilitated via Rsubread function wrappers to index the new
reference, align user FASTA sequences to it, and then perform
quantification for desired features (e.g. exon, utr, etc.)
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: Annotation, RNASeq, Alignment, MultipleSequenceAlignment, QualityControl, Preprocessing, Sequencing, DataImport, GeneExpression
Imports: Rsubread (>= 2.14.2), Biostrings (>= 2.68.1), rtracklayer (>= 1.60.0), GenomicRanges (>= 1.52.0), tools, utils
Suggests:
Rsamtools,
BiocStyle,
knitr,
rmarkdown,
testthat (>= 3.0.0)
URL: https://gitlab.com/mtekman/CustomGenome
BugReports: https://gitlab.com/mtekman/CustomGenome/issues
Config/testthat/edition: 3
jorainer
mtekman
lshep
PeteHaitch
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