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update vignettes, microbiome tutorials, description #6

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Merged
JialinGao111 merged 3 commits into from
Apr 1, 2025
Merged

update vignettes, microbiome tutorials, description #6

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66ecb88
Merge pull request #2 from himelmallick/master
JialinGao111 Mar 21, 2025
b3f6dab
Updated Microbiome tutorial rmd and html and update some new datasets
JialinGao111 Mar 21, 2025
d6b967a
Passed devtools check with no errors, update vignette
JialinGao111 Apr 1, 2025
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5,534 changes: 5,534 additions & 0 deletions Codes/Dataset/hmp2_metadata_2018-08-20.csv
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95 changes: 95 additions & 0 deletions Codes/Dataset/metadata_baseline.csv
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1,480 changes: 1,480 additions & 0 deletions Codes/Dataset/metaphlan3_taxonomic_profiles.tsv
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5,241 changes: 5,241 additions & 0 deletions Codes/Dataset/metaphlan4_taxonomic_profiles.tsv
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1,790 changes: 1,790 additions & 0 deletions Codes/Dataset/taxa_table_baseline.csv
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25 changes: 18 additions & 7 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: DAssemble
Type: Package
Title: Ensemble models for differential analysis
Version: 0.0.1
Version: 0.99.0
Authors@R:
c(
person("Himel", "Mallick", email = "him4004@med.cornell.edu", role = c("aut", "cre")),
Expand All @@ -15,22 +15,33 @@ Description:
License: MIT + file LICENSE
Encoding: UTF-8
biocViews:
DifferentialExpression
DifferentialExpression,
Software,
RNASeq,
Microbiome
Imports:
metapod,
poolr,
harmonicmeanp,
dplyr
Suggests:
DESeq2,
airway,
edgeR,
limma,
tidyverse,
dplyr
Suggests:
airway,
limma,
testthat,
knitr,
rmarkdown,
BiocStyle
BiocStyle,
Seurat,
KernSmooth,
foreign,
nnet,
rpart,
spatial,
boot,
class
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2.9000
VignetteBuilder: knitr
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