miLineage: An R package to perform association tests for microbial lineages on a taxonomic tree
https://medschool.vanderbilt.edu/tang-lab/software/miLineage
citation: Tang ZZ, Chen G, Alekseyenko AV, Li H (2016). A general framework for association analysis of microbial communities on a taxonomic tree. Bioinformatics. btw804.
miProfile: A C program for analyzing microbial community composition
https://medschool.vanderbilt.edu/tang-lab/software/miProfile
citation: Tang ZZ, Chen G, Alekseyenko AV (2016). PERMANOVA-S: Association test for microbial community composition that accommodates confounders and multiple distances, Bioinformatics, btw311.
PreMeta: A C program to facilitate the exchange of information between four software packages for meta-analysis of rare-variant associations: MASS, RAREMETAL, MetaSKAT, and seqMeta.
http://dlin.web.unc.edu/software/premeta/
MASS: A C program for the meta-analysis of sequencing studies.
http://dlin.web.unc.edu/software/mass/
SCORE-SeqTDS: A C program for analyzing primary and secondary traits in sequencing studies under trait- dependent sampling.
http://dlin.web.unc.edu/software/score-seqtds/
SCORE-Seq: A C program which implements score statistics for detecting disease associations with rare variants in sequencing studies.
http://dlin.web.unc.edu/software/score-seq/
genoCN: An R package for identifying copy number states and genotype calls using the SNP arrays data.
https://www.bioconductor.org/packages/release/bioc/html/genoCN.html