Sequence Error Filtering Pipeline for FFPE Samples
person(given = "Masachika",
family = "Ikegami",
role = c("aut", "cre"),
email = "ikegamitky@gmail.com")
Clinical sequencing of tumor is usually performed on formalin-fixed
and paraffin-embedded (FFPE) samples and have many sequencing errors. We
found that the majority of these errors are detected in chimeric read
caused by single-strand DNA with microhomology. Our filtering pipeline
focuses on the uneven distribution of the artifacts in each read and removes
such errors in FFPE samples without over-eliminating the true mutations
detected in fresh frozen samples.
tidyr, openxlsx, data.table, R.utils, stringr, magrittr,
dplyr, gtools, Biostrings, GenomicAlignments, Rsamtools,
GenomeInfoDb, BiocGenerics
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, knitr, rmarkdown

Deploys your R Analytic to MicroStrategy
c(person(given="Rick", family="Pechter",
email="rpechter@microstrategy.com", role=c("aut", "cre")))

Statistical Methods for Microbiome Compositional Data
c(
person("Xianyang", "Zhang", role = "aut", email = "zhangxiany@stat.tamu.edu"),
person("Jun", "Chen", role = c("aut", "cre"),
email = "chen.jun2@mayo.edu"),
person("Huijuan", "Zhou", role = "ctb"))
Xianyang Zhang [aut],
Jun Chen [aut, cre],
Huijuan Zhou [ctb]
A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects (Zhou et al. (2021)<arXiv:2104.00242>).  The methods can be applied to the analysis of other (high-dimensional) compositional data arising from sequencing experiments.
ggplot2, matrixStats, Matrix, parallel, stats, utils, statmod,
MASS, ggrepel, lmerTest, foreach, modeest

ggplot2, matrixStats, Matrix, parallel, stats, utils, statmod,
MASS, ggrepel, lmerTest, foreach, modeest, phyloseq

Interface to the 'Microsoft 365' Suite of Cloud Services
An interface to the 'Microsoft 365' (formerly known as 'Office 365') suite of cloud services, building on the framework supplied by the 'AzureGraph' package. Enables access from R to data stored in 'SharePoint Online' and 'OneDrive', including the ability to list drive folder contents, upload and download files, and retrieve data lists. Both personal 'OneDrive' and 'OneDrive for Business' accounts are supported.
AzureAuth, AzureGraph (>= 1.2.0), utils, curl, httr, jsonlite,
R6, vctrs