bioc-issue-bot
commented
2 years ago Hi @snikumbh
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:
Type: Package
Package: seqArchR
Title: Identify Different Architectures of Sequence Elements
Version: 0.99.0
Authors@R:
person("Sarvesh", "Nikumbh", email = "sarvesh.nikumbh@gmail.com",
role = c("aut", "cre", "cph"),
comment = c(ORCID = "0000-0003-3163-4447",
Twitter = "@sarveshnikumbh"))
Description: \code{seqArchR} enables unsupervised discovery of _de novo_ clusters
with characteristic sequence architectures characterized by
position-specific motifs or composition of stretches of nucleotides,
e.g., CG-richness. \code{seqArchR} does _not_ require any specifications
w.r.t. the number of clusters, the length of any individual motifs, or
the distance between motifs if and when they occur in pairs/groups; it
directly detects them from the data. \code{seqArchR} uses non-negative
matrix factorization (NMF) as its backbone, and employs a chunking-based
iterative procedure that enables processing of large sequence collections
efficiently. Wrapper functions are provided for visualizing cluster
architectures as sequence logos.
License: GPL-3 | file LICENSE
URL: https://snikumbh.github.io/seqArchR/,
https://github.com/snikumbh/seqArchR
BugReports: https://github.com/snikumbh/seqArchR/issues
SystemRequirements: Python (>= 3.5), scikit-learn (>= 0.21.2)
Depends:
R (>= 4.1.0)
Imports:
utils,
graphics,
cvTools (>= 0.3.2),
MASS,
Matrix,
methods,
stats,
cluster,
matrixStats,
fpc,
cli,
prettyunits,
reshape2 (>= 1.4.3),
reticulate (>= 1.22),
parallel,
Biostrings,
grDevices,
ggplot2 (>= 3.1.1),
ggseqlogo (>= 0.1)
Suggests:
TFBSTools,
cowplot,
hopach (>= 2.42.0),
knitr (>= 1.22),
rmarkdown (>= 1.12),
testthat (>= 3.0.2),
covr,
vdiffr (>= 0.3.0)
VignetteBuilder:
knitr
biocViews:
MotifDiscovery,
GeneRegulation,
MathematicalBiology,
SystemsBiology,
Transcriptomics,
Genetics,
Clustering,
DimensionReduction,
FeatureExtraction,
DNASeq
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.2
snikumbh
jianhong
lshep
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