From 5d35f16db876b912047b1323c50fe8e9041be8b2 Mon Sep 17 00:00:00 2001
From: caoyang <yiluheihei@gmail.com>
Date: Sun, 9 Feb 2025 20:05:15 +0800
Subject: [PATCH] bump version to 1.13.1

---
 DESCRIPTION                     |  5 ++---
 man/extract_posthoc_res.Rd      |  8 ++++----
 man/microbiomeMarker-package.Rd | 12 ++++++++++++
 man/run_edger.Rd                |  4 ++--
 4 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f5127f2..2967aec 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: microbiomeMarker
 Title: microbiome biomarker analysis toolkit
-Version: 1.13.0
+Version: 1.13.1
 Authors@R: 
     person(given = "Yang",
            family = "Cao",
@@ -60,7 +60,7 @@ Imports:
     pROC,
     BiocParallel
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Suggests: 
     testthat,
@@ -76,4 +76,3 @@ Suggests:
     withr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-PackageStatus: Deprecated
diff --git a/man/extract_posthoc_res.Rd b/man/extract_posthoc_res.Rd
index cc49982..40a9baf 100644
--- a/man/extract_posthoc_res.Rd
+++ b/man/extract_posthoc_res.Rd
@@ -24,8 +24,8 @@ require(IRanges)
 pht <- postHocTest(
     result = DataFrameList(
         featureA = DataFrame(
-            comparisons = c("group2-group1", 
-                "group3-group1", 
+            comparisons = c("group2-group1",
+                "group3-group1",
                 "group3-group2"),
             diff_mean = runif(3),
             pvalue = rep(0.01, 3),
@@ -33,8 +33,8 @@ pht <- postHocTest(
             ci_upper = rep(0.011, 3)
         ),
         featureB = DataFrame(
-            comparisons = c("group2-group1", 
-                "group3-group1", 
+            comparisons = c("group2-group1",
+                "group3-group1",
                 "group3-group2"),
             diff_mean = runif(3),
             pvalue = rep(0.01, 3),
diff --git a/man/microbiomeMarker-package.Rd b/man/microbiomeMarker-package.Rd
index 6d2cdb1..3e1b441 100644
--- a/man/microbiomeMarker-package.Rd
+++ b/man/microbiomeMarker-package.Rd
@@ -7,5 +7,17 @@
 \description{
 The microboimeMarker package provides several methods to identify micribome
 biomarker, such as lefse, deseq2.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/yiluheihei/microbiomeMarker}
+  \item Report bugs at \url{https://github.com/yiluheihei/microbiomeMarker/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Yang Cao \email{caoyang.name@gmail.com}
+
 }
 \keyword{internal}
diff --git a/man/run_edger.Rd b/man/run_edger.Rd
index cd1eabc..8887d4a 100644
--- a/man/run_edger.Rd
+++ b/man/run_edger.Rd
@@ -89,7 +89,7 @@ for more details see \link[stats:p.adjust]{stats::p.adjust}.}
 
 \item{pvalue_cutoff}{numeric, p value cutoff, default 0.05}
 
-\item{...}{extra arguments passed to the model. See \code{\link[edgeR:glmQLFTest]{edgeR::glmQLFit()}}
+\item{...}{extra arguments passed to the model. See \code{\link[edgeR:glmQLFit]{edgeR::glmQLFit()}}
 and \code{\link[edgeR:glmfit]{edgeR::glmFit()}} for more details.}
 }
 \value{
@@ -137,7 +137,7 @@ Bioconductor package for differential expression analysis of digital
 gene expression data." Bioinformatics 26.1 (2010): 139-140.
 }
 \seealso{
-\code{\link[edgeR:glmfit]{edgeR::glmFit()}},\code{\link[edgeR:glmQLFTest]{edgeR::glmQLFit()}},\code{\link[edgeR:estimateDisp]{edgeR::estimateDisp()}}
+\code{\link[edgeR:glmfit]{edgeR::glmFit()}},\code{\link[edgeR:glmQLFit]{edgeR::glmQLFit()}},\code{\link[edgeR:estimateDisp]{edgeR::estimateDisp()}}
 ,\code{\link[=normalize]{normalize()}}
 }
 \author{