Closed Lionir closed 3 years ago
Hi @Lionir
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: octad
Title: Open Cancer TherApeutic Discovery (OCTAD)
Version: 0.99.0
Authors@R:
c(person(given = "E.",
family = "Chekalin",
role = c("aut", "cre"),
email = "eygen.chekalin@gmail.com"),
person(given = "B.",
family = "Zeng",role =c("aut")),
person(given = "B.",
family = "Glicksberg",role ="ctb"),
person(given = "P.",
family = "Newbury",role ="ctb"),
person(given = "J.",
family = "Xing",role ="ctb"),
person(given = "K.",
family = "Liu",role ="ctb"),
person(given = "A.",
family = "Wen",role ="ctb"),
person(given = "D.",
family = "Joseph",role ="ctb"),
person(given = "B.",
family = "Chen",
role ="aut",
email = "chenbi12@msu.edu")
)
Description: OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Depends:
R (>= 4.0),
magrittr,
dplyr,
ggplot2,
edgeR,
RUVSeq,
DESeq2,
limma,
rhdf5,
doParallel,
foreach,
Rfast,
octad.db,
stats,
httr
Imports:
EDASeq,
GSVA,
data.table,
htmlwidgets,
plotly,
reshape2
Suggests:
knitr,
rmarkdown
VignetteBuilder: knitr
biocViews: Classification, GeneExpression, Pharmacogenetics, Pharmacogenomics, Software
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Your package has been built on Linux, Mac, and Windows.
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Do you plan on following up with this submission?
Dear Sir,
Ies I do, but it's currently impossible to get rid of octad.db since it contains relevant files to computation. Should I re-submit is as experimentalhub package first and only then attach the initial package? Or maybe it is possible to avoid this process since we have the package stored on the AWS server and it is possible to install it from the web?
Thank you in advance.
Best wishes, Evgeny Chekalin, PhD, Research associate,
Michigan State University, College of Human Medicine
Department of Pediatrics and Human Development Secchia Center, room 732 15 Michigan St. NE Grand Rapids, MI 49503 +1(616) 617-1746
On Tue, Oct 27, 2020 at 7:40 AM lshep notifications@github.com wrote:
Do you plan on following up with this submission?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1679#issuecomment-717183930, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJQPWNYIMY6BXCB7HGVKKSDSM2WR7ANCNFSM4SBFL5ZA .
You will need to submit the octad.db as an additional package. We do not allow packages on our build system to be downloaded from any other location than from CRAN or Bioconductor.
Got you, will do it by tomorrow.
Best wishes, Evgeny Chekalin, PhD, Research associate,
Michigan State University, College of Human Medicine
Department of Pediatrics and Human Development Secchia Center, room 732 15 Michigan St. NE Grand Rapids, MI 49503 +1(616) 617-1746
On Tue, Oct 27, 2020 at 1:14 PM lshep notifications@github.com wrote:
You will need to submit the octad.db as an additional package. We do not allow packages on our build system to be downloaded from any other location than from CRAN or Bioconductor.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1679#issuecomment-717393879, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJQPWN5TIKBUCCZ7I4ONZA3SM35VVANCNFSM4SBFL5ZA .
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