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DESCRIPTION
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DESCRIPTION
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Package: deq
Title: A package to conveniently run DESeq2, edgeR, and QNB for the detection of differential methylation in MeRIP/m6A-seq data.
Version: 0.0.1
Authors@R: person("A", "McIntyre", email = "abm237@cornell.edu", role = c("aut", "cre"))
Description: Predicts differential methylation by implementing generalized linear models in DESeq2 or edgeR, or by running QNB.
Depends: R (>= 3.5.0)
License: MIT
Encoding: UTF-8
LazyData: true
Imports:
AnnotationDbi (>= 1.44.0),
BiocParallel (>= 1.14.2),
data.table (>= 1.11.4),
DESeq2 (>= 1.20.0),
plyr (>= 1.8.4),
dplyr (>= 0.7.6),
edgeR (>= 3.22.3),
GenomicFeatures (>= 1.32.2),
GenomeInfoDb (>= 1.16.0),
GenomicRanges (>= 1.32.6),
QNB (>= 1.1.11),
Rsamtools (>= 1.32.3),
Rsubread (>= 1.30.5),
rtracklayer (>= 1.40.6),
S4Vectors
RoxygenNote: 6.1.1
Collate:
'count_reads.R'
'import_peaks.R'
'metdiff_function_copy.R'
'run_tools.R'
'run_deq_pipeline.R'