DESCRIPTION

Package: RepAn
Type: Package
Version: 0.1.1
Date: 2018-07-26
Author: Dawit A. Yohannes
Maintainer: Dawit A. Yohannes <dawit.yohannes@helsinki.fi>
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 
    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),
    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