From 47455176e74e5844671b1e3caf406647697728e4 Mon Sep 17 00:00:00 2001 From: "Dawit A. Yohannes" Date: Thu, 10 Jul 2025 16:38:09 +0300 Subject: [PATCH 1/6] Update DESCRIPTION removed wordspace package --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f0425d3..a571d98 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,7 +24,6 @@ Depends: preprocessCore (>= 1.32.0), randomForest (>= 4.6-12), gplots (>= 3.0.1), - wordspace (>= 0.2-0), e1071 (>= 1.6-7), data.table (>= 1.9.6), gplots (>= 3.0.1), From b67d61cdddfccc14d19f996cc3860f82623dee49 Mon Sep 17 00:00:00 2001 From: "Dawit A. Yohannes" Date: Thu, 10 Jul 2025 16:41:13 +0300 Subject: [PATCH 2/6] Update DESCRIPTION --- DESCRIPTION | 1 - 1 file changed, 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index a571d98..554ef81 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -46,7 +46,6 @@ Imports: preprocessCore (>= 1.32.0), randomForest (>= 4.6-12), gplots (>= 3.0.1), - wordspace (>= 0.2-0), e1071 (>= 1.6-7), data.table (>= 1.9.6), gplots (>= 3.0.1), From a553d53510be2dbce5b9e4532ef388cc1ae2df03 Mon Sep 17 00:00:00 2001 From: "Dawit A. Yohannes" Date: Sat, 26 Jul 2025 14:48:38 +0300 Subject: [PATCH 3/6] Update DESCRIPTION --- DESCRIPTION | 2 -- 1 file changed, 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 554ef81..812fd39 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,6 @@ Depends: ggplot2 (>= 1.0.0), cluster (>= 2.0.5), Biostrings (>= 2.38.4), - RankProd (>= 2.42.0), doParallel (>= 1.0.10), parallel, preprocessCore (>= 1.32.0), @@ -40,7 +39,6 @@ Imports: ggplot2 (>= 1.0.0), cluster (>= 2.0.5), Biostrings (>= 2.38.4), - RankProd (>= 2.42.0), doParallel (>= 1.0.10), parallel, preprocessCore (>= 1.32.0), From 8bb3f2aa91ecc3e57f68374af04a327d41f809b2 Mon Sep 17 00:00:00 2001 From: "Dawit A. Yohannes" Date: Sat, 26 Jul 2025 14:54:37 +0300 Subject: [PATCH 4/6] Update DESCRIPTION --- DESCRIPTION | 29 +++-------------------------- 1 file changed, 3 insertions(+), 26 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 812fd39..e276331 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,12 +7,13 @@ Maintainer: Dawit A. Yohannes URL: https://www.helsinki.fi/en/researchgroups/immunomics Title: Differential abundance Analysis for deep sequenced immune repertoire (Repseq) datasets Description: RepAn mainly performs differential abundance analysis by comparing immune repertoire - samples in two conditon groups to find condition associated CDR3 sequences. It conducts the comparison between sample groups + samples in two condition groups to find condition associated CDR3 sequences. It conducts the comparison between sample groups at population level at the level of sub-repertoires, which are clusters of CDR3s that have shared immuno-genomic features across samples. RepAn also implements basic analysis functions for immune repertoire datasets. License: GPL-3 Depends: - R (>= 2.15.1), + R (>= 2.15.1) +Suggests: Matrix (>= 1.2-7.1), dynamicTreeCut, ggplot2 (>= 1.0.0), @@ -25,36 +26,12 @@ Depends: gplots (>= 3.0.1), e1071 (>= 1.6-7), data.table (>= 1.9.6), - gplots (>= 3.0.1), - kmer (>= 1.0.2), - dendextend (>= 1.3.0), - ape (>= 5.1), - RankProd, - preprocessCore, - ggseqlogo (>= 0.1), - fclust -biocViews: -Imports: - dynamicTreeCut, - ggplot2 (>= 1.0.0), - cluster (>= 2.0.5), - Biostrings (>= 2.38.4), - doParallel (>= 1.0.10), - parallel, - preprocessCore (>= 1.32.0), - randomForest (>= 4.6-12), - gplots (>= 3.0.1), - e1071 (>= 1.6-7), - data.table (>= 1.9.6), - gplots (>= 3.0.1), kmer (>= 1.0.2), dendextend (>= 1.3.0), ape (>= 5.1), RankProd, - preprocessCore, ggseqlogo (>= 0.1), fclust LazyData: true RoxygenNote: 6.1.0 Encoding: UTF-8 - From db0e38eb884064fbc2a380d999dc5de443aa2fce Mon Sep 17 00:00:00 2001 From: "Dawit A. Yohannes" Date: Sat, 26 Jul 2025 14:55:47 +0300 Subject: [PATCH 5/6] Update NAMESPACE --- NAMESPACE | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 801bbee..f157bc8 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,18 +1,3 @@ # Generated by roxygen2: do not edit by hand exportPattern("^[^\\.]") -import(Matrix) -import(cluster) -import(kmer) -import(wordspace) -import(parallel) -import(doParallel) -import(gplots) -import(ggplot2) -importFrom(ape,as.AAbin) -importFrom(fclust,SIL) -importFrom(dynamicTreeCut,cutreeDynamic) -importFrom(randomForest,randomForest) -importFrom(randomForest,importance) -importFrom(e1071,cmeans) -importFrom(data.table,fread) From ac8d495ae0b01cb0f2621101597b5fd37a4968c8 Mon Sep 17 00:00:00 2001 From: "Dawit A. Yohannes" Date: Sat, 26 Jul 2025 15:03:52 +0300 Subject: [PATCH 6/6] Update README.md installation from dev branch --- README.md | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 9e5721f..e6e44cd 100644 --- a/README.md +++ b/README.md @@ -11,16 +11,9 @@ put through a ranking based filtering to identify the most likely condition asso For detailed description of the differential abundance analysis method, please see (https://doi.org/10.1186/s12859-021-04087-7) ## Installation -To install RepAn package in R, first install R devtools package and run its install_github function as follows: - -``` -install.packages("devtools") -devtools::install_github("dyohanne/RepAn") -``` -If installing R package dependencies with the previous command gives errors, first install RepAn without the dependencies and use the package installation functions that come with RepAn as follows: - +To install RepAn package in R, first install RepAn from the development branch without the dependencies and use the package installation functions that come with RepAn as follows: ``` -devtools::install_github("dyohanne/RepAn",dependencies=F) +devtools::install_github("dyohanne/RepAn@development", dependencies = FALSE, upgrade = "never") loadPacks() loadBioconductorPacks() ```