diff --git a/DESCRIPTION b/DESCRIPTION index f0425d3..e276331 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,58 +7,31 @@ 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), cluster (>= 2.0.5), Biostrings (>= 2.38.4), - RankProd (>= 2.42.0), doParallel (>= 1.0.10), parallel, 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), - 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), - RankProd (>= 2.42.0), - doParallel (>= 1.0.10), - parallel, - 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), 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 - 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) 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() ```