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.

Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).

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.

S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.

Based on the structure of the SPSS version of the Swiss
    Household Panel (SHP) data, provides a function seqFromWaves()
    that seeks the data of variables specified by the user in each 
    of the wave files and collects them as sequences. The function also 
    matches the sequences with variables from other files such as the 
    master files of persons (MP) and households (MH), and social origins (SO). 
    It can also match with activity calendar data (CA).