Multiple imputation of missing data in a dataset using MICT or 
    MICT-timing methods. The core idea of the algorithms is to fill gaps of 
    missing data, which is the typical form of missing data in a longitudinal 
    setting, recursively from their edges. Prediction is based on either a 
    multinomial or random forest regression model. Covariates and 
    time-dependent covariates can be included in the model.

Exploratory data analysis and data visualization
  for biological sequence (DNA and protein) data. Seqinr includes
  utilities for sequence data management under the ACNUC system
  described in Gouy, M. et al. (1984) Nucleic Acids Res.
  12:121-127 <doi:10.1093/nar/12.1Part1.121>.

Kataegis is a localized hypermutation occurring when a region is enriched in somatic SNVs. Kataegis can result from multiple cytosine deaminations catalyzed by the AID/APOBEC family of proteins. This package contains functions to detect kataegis from SNVs in BED format. This package reports two scores per kataegic event, a hypermutation score and an APOBEC mediated kataegic score. Yousif, F. et al.; The Origins and Consequences of Localized and Global Somatic Hypermutation; Biorxiv 2018 <doi:10.1101/287839>.

A network module-based generalized linear model for differential expression analysis with the count-based sequence data from RNA-Seq.

Tools for reading and writing biological sequences in multiple
    formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and
    'GenBank'. Supports interleaved and sequential layouts where applicable,
    converts between formats, and manipulates sequence sets (e.g., filtering by
    patterns and computing consensus sequences from alignments). Also includes
    functions to download nucleotide records from NCBI by accession.

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read 'RareMETAL' summary statistics files; (3) read tables from a 'tabix'-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.