bioc-issue-bot
commented
1 year ago Hi @YuePan027
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: MICSQTL
Type: Package
Title: MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
Version: 0.99.2
Authors@R: c(person("Yue", "Pan", role = c("aut", "cre"),
email = "Yue.Pan@STJUDE.ORG"),
person("Qian", "Li", role = "aut",
email = "Qian.Li@STJUDE.ORG"))
Description: Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.
License: GPL-3
Encoding: UTF-8
Suggests:
testthat,
rmarkdown,
knitr
VignetteBuilder: knitr
biocViews: GeneExpression, Genetics, Proteomics, RNASeq, Sequencing, SingleCell, Software, Visualization, CellBasedAssays
Imports:
TCA,
nnls,
e1071,
preprocessCore,
tidyverse,
tibble,
purrr,
TOAST,
magrittr,
BiocParallel,
ggplot2,
ggpubr,
ggridges,
parallel,
glue,
methods
Depends:
R (>= 4.2.0),
SummarizedExperiment,
stats
RoxygenNote: 7.2.1
LazyData: false
YuePan027
lshep
jianhong
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