bioc-issue-bot
commented
3 years ago Hi @Danis102
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: seqpac
Type: Package
Title: seqpac - Group-based Analysis of Short Reads Using Sequence Counts
Version: 0.99.0
Authors@R: c(
person("Daniel", "Natt", email="daniel.natt@liu.se", role= c("aut", "cre", "fnd")),
person("Lovisa", "Örkenby", email="lovisa.orkenby@liu.se", role= "ctb"),
person("Signe", "Skog", email="signe.skog@liu.se", role= "ctb"),
person("Anita", "Öst", email="anita.ost@liu.se", role= c("aut", "fnd"))
)
Description: A collection of functions used for complete analysis of short sequenced reads.
The package was originally developed for small RNA analysis, but can be implemented on
any sequencing raw data (provided as a fastq-file) where intended unit of measurement
is counts of unique sequences. The core of the seqpac workflow is the generation and
subsequence analysis/visualization of a standardized list object called PAC. Using an
innovative target system, seqpac extracts, analyze and visualize group differences
using the PAC object.
A PAC object in its most basic form is a list containing three types of data frames:
- Phenotype table (P): Sample names (rows) with associated metadata (columns) e.g. groups.
- Annotation table (A): Unique sequences (rows) with annotation (columns), eg. reference alignment.
- Counts table (C): Counts of unique sequences (rows) for each sample (columns).
The PAC list-objects follow the rule:
- Row names in P must be identical with column names in C.
- Row names in A must be identical with row names in C.
Thus P and A describes the columns and rows in C, respectively. The targeting system, will either
target specific samples in P (pheno_target) or sequences in A (anno_target) and group them according
to a target column in P and A, respectively.
License: GLP-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
URL: https://github.com/Danis102/seqpac
BugReports: https://github.com/Danis102/seqpac/issues
biocViews:
Workflow
EpigeneticWorkflow
AnnotationWorkflow
GeneExpressionWorkflow
Depend:
Biostrings (>= 2.46.0),
foreach (>= 1.5.1),
GenomicRanges (>= 1.30.3,
Rbowtie (>= 1.18.0),
ShortRead (>= 1.36.1),
tibble (>= 3.1.2)
Imports:
BiocParallel (>= 1.12.0),
Biostrings (>= 2.46.0),
cowplot (>= 0.9.4),
data.table (>= 1.14.0),
digest (>= 0.6.27),
doParallel (>= 1.0.16),
dplyr (>= 1.0.6),
factoextra (>= 1.0.7),
FactoMineR (>= 1.41),
foreach (>= 1.5.1),
GenomicRanges (>= 1.30.3),
ggplot2 (>= 3.3.3),
IRanges (>= 2.12.0),
parallel (>= 3.4.4),
Rbowtie (>= 1.18.0),
readr (>= 1.4.0),
reshape2 (>= 1.4.4),
rtracklayer (>= 1.38.3),
ShortRead (>= 1.36.1),
stringr (>= 1.4.0),
stats (>= 3.4.4),
tibble (>= 3.1.2),
tidyr (>= 1.1.3)
Suggests:
benchmarkme (>= 0.6.0),
DESeq2 (>= 1.18.1),
GenomeInfoDb (>= 1.14.0),
gginnards (>= 0.0.2),
knitr,
qqman (>= 0.1.8),
rmarkdown,
testthat,
UpSetR (>= 1.4.0),
venneuler
VignetteBuilder:
knitr
jianhong
lshep
Danis102
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