Mediation analysis in the presence of high-dimensional mediators based on the potential
outcome framework. Bayesian Mediation Analysis (BAMA), developed by Song et al (2018)
<doi:10.1101/467399>.
Reference: Skol, A.D., Scott, L.J., Abecasis, G.R. and Boehnke, M., 2006. Joint analysis is
more efficient than replication-based analysis for two-stage genome-wide association
studies. Nature Genetics, 38(2), p.209.
chipenrich
Performs gene set enrichment for ChIP-seq peak data.
Reference: Welch RP, Lee C, Cavalcante RG, Smith RA, Imbriano P, Scott LJ, Sartor MA (2014).
“ChIP-Enrich: Gene set enrichment testing for ChIP-Seq data.” Nucleic Acids Research.
CisGenome Browser
A flexible stand-alone tool for genomic data visualization.
Reference: Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers and Wing H.
Wong (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Nature Biotechnology, 26: 1293-1300. doi:10.1038/nbt.1505.
cleancall
Correction for DNA contamination in genotype calling.
CopyMap is based on a hidden Markov Model (HMM), predicting the location of CNVs and
their allele frequencies using data from a set of CGH experiments.
Reference: Wen, X., Lee, Y., Luca, F., Pique-Regi, R. Efficient Integrative Multi-SNP Association
Analysis using Deterministic Approximation of Posteriors. The American Journal of
Human Genetics, 98(6), 1114-1129.
DPR
DPR is a software package implementing the latent Dirichlet process regression method
for genetic prediction of complex traits.
Reference: Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E.
(2010) Variance component model to account for sample structure in genome-wide association
studies. Nat. Genet. 42:348-54.
EPACTS
Efficient and Parallelizable Association Container Toolbox. Perform various statistical
tests for identifying genome-wide association from sequence data through a user-friendly
interface.
References: Reppell, M., Boehnke, M. and Zöllner, S., 2012. FTEC: a coalescent simulator for modeling
faster than exponential growth. Bioinformatics, 28(9), pp.1282-1283.
FUGUE
Construct haplotypes for the chromosome 22 and 19 linkage disequilibrium maps.
Genetic Association Study (GAS) Power Calculator interface that can be used to compute
statistical power for large one-stage genetic association studies.
Reference: Johnson, J.L. and Abecasis, G.R., 2017. GAS Power Calculator: web-based power calculator
for genetic association studies. bioRxiv, p.164343.
GEMMA
GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association
algorithm for a standard linear mixed model and some of its close relatives for genome-wide
association studies (GWAS).
Reference: Gao, X., Pu, DQ., & Song, P.X.K. (2009). Transition dependency: a gene-gene interactionmeasure
for times seriesmicroarray data. EURASIP Journal on Bioinformatics and Systems Biology,
2009, 2.
GRR is a Windows-based application for detecting pedigree errors via graphically inspecting
the distribution for marker allele sharing among pairs of family members or all pairs
of individuals in a study.
Reference: Yue Fan, Tauras P. Vilgalys, Shiquan Sun, Qinke Peng, Jenny Tung and Xiang Zhou (2019).
High-powered detection of genetic effects on DNA methylation using integrated methylation
QTL mapping and allele-specific analysis. bioRxiv.
iMAP
iMAP is a method which performs integrative mapping of pleiotropic association and
functional annotations using penalized Gaussian mixture models.
Reference: Wen, X., Pique-Regi, R., Luca, F. Integrating Molecular QTL Data into Genome-wide
Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization.
PLOS Genetics. 2017 Mar 13(3): e1006646.
LAMP
LAMP is our software for Linkage and Association Modeling in Pedigrees.
Reference: Li, M., Boehnke, M. and Abecasis, G.R., 2005. Joint modeling of linkage and association:
identifying SNPs responsible for a linkage signal. The American Journal of Human Genetics,
76(6), pp.934-949.
LASER
Estimate genetic ancestry on reference maps of diverse populations.
References: He et al. (2017) "Set-Based Tests for Gene-Environment Interaction in Longitudinal
Studies" and He et al. (2017) "Rare-variant association tests in longitudinal studies,
with an application to the Multi-Ethnic Study of Atherosclerosis (MESA)".
LocusZoom
Plot regional association results from genome-wide association scans.
Reference: Abecasis, G.R., Cherny, S.S., Cookson, W.O. and Cardon, L.R., 2001. Merlin—rapid analysis
of dense genetic maps using sparse gene flow trees. Nature Genetics, 30(1), p.97.
Metal
METAL software is designed to facilitate meta-analysis of large datasets (such as
several whole genome scans) in a convenient, rapid and memory efficient manner.
Reference: Willer, C.J., Li, Y. and Abecasis, G.R., 2010. METAL: fast and efficient meta-analysis
of genomewide association scans. Bioinformatics, 26(17), pp.2190-2191.
MetaSKAT
MetaSKAT is an R package for gene-based meta-analysis across studies. It can carry
out a meta-analysis of SKAT, SKAT-O and burden tests with individual-level genotype
data or gene-level summary statistics.
PMR-Egger is a method that fits probabilistic Mendelian randomization with an Egger
regression assumption on horizontal pleiotropy for transcriptome-wide association
studies (TWASs).
Reference: Zhongshang Yuan, Huanhuan Zhu, Ping Zeng, Sheng Yang, Shiquan Sun, Can Yang, Jin Liu
and Xiang Zhou (2019). Testing and controlling for horizontal pleiotropy with the
probabilistic Mendelian randomization in transcriptome-wide association studies.
PRSweb
Interactive PheWAS results from analyses conducted using Michigan Genomics Initiative
and UK Biobank data.
Reference: Abecasis, G.R., Cardon, L.R. and Cookson, W.O.C., 2000. A general test of association
for quantitative traits in nuclear families. The American Journal of Human Genetics,
66(1), pp.279-292.
RAREMETAL
Meta-analysis of rare variants from genotype arrays or sequencing.
RELPAIR 2.0.1 is a FORTRAN 77 program that infers the relationships of pairs of individuals
based on genetic marker data, either within families or across an entire sample.
Reference: Epstein MP, Duren WL and Boehnke M (2000) Improved inference of relationships for
pairs of individuals. American Journal of Human Genetics 67:1219-1231.
RHMAP
RHMAP 3.0 (updated September 1996) is a statistical package for radiation hybrid mapping.
Reference: Boehnke M, Lunetta K, Hauser E, Lange K, Uro J, and VanderStoep J. RHMAP: Statistical
Package for Multipoint Radiation Version 3.0, September 1996.
rSeqNP
A non-parametric approach for detecting differential expression and splicing from
RNA-Seq data.
Reference: Shi, Y., Chinnaiyan, A. M., Jiang, H. (2015) rSeqNP: A non-parametric approach for
detecting differential ex-pression and splicing from RNA-Seq data Bioinformatics,
in press.
rSeqDiff
Detecting differential isoform expression from RNA-seq data.
Reference: Shi, Y., Jiang, H. (2013). rSeqDiff: Detecting differential isoform expression from
RNA-Seq data using hierarchical likelihood ratio test, PLoS One, 8 (11): e79448.
rSeq
rSeq is a set of tools for RNA-Seq data analysis. It consists of programs that deal
with many aspects of RNA-Seq data analysis, such as read quality assessment, reference
sequence generation, sequence mapping, gene and isoform expressions (RPKMs) estimation,
etc.
References: [1] Jiang, H., Wong, W.H. (2009) Statistical Inferences for Isoform Expression in
RNA-Seq, Bioinformatics, 25(8), 1026–1032. [2] Salzman, J., Jiang, H., Wong, W. H.
(2011) Statistical Modeling of RNA-Seq Data, Statistical Science, 26 (1): 62-83.
SAIGE
SAIGE is an R-package for testing for associations between genetic variants and binary
phenotypes with adjusting for sample relatedness and case-control imbalance.
References: John C. Mu, Hui Jiang, Amirhossein Kiani, Marghoob Mohiyuddin, Narges Bani Asadi
and Wing H. Wong, Fast and Accurate Read Alignment for Resequencing, Bioinformatics,
2012.
SeqMap
A tool for mapping millions of short sequences to the genome.
Reference: Douglas J.A. and Boehnke M. SIBMED: A Program that Identifies Likely Genotyping Errors
and Mutations for a Sib Pair in the Context of Multipoint Mapping Version 1.0, April
18, 2000.
SIMLINK
SIMLINK 4.12 (updated April 1997) is a program for estimating the power of a proposed
linkage study by computer simulation.
SKAT is an R-package for rare variant association analysis. It can carry out burden
test, SKAT, SKAT-O, and combined test of common and rare variants with adjusting for
covariates and kinship. For binary traits, it can calculate p-values using resampling
and asymptotic based adjustment methods. It also has functions for sample size and
power calculations.
Reference: Wigginton, J.E., Cutler, D.J. and Abecasis, G.R., 2005. A note on exact tests of Hardy-Weinberg
equilibrium. The American Journal of Human Genetics, 76(5), pp.887-893.
SPARK
SPARK is a method for detecting genes with spatial expression patterns in spatially
resolved transcriptomic studies.
Reference: Shiquan Sun*, Jiaqiang Zhu* and Xiang Zhou (2019). Statistical analysis of spatial
expression pattern for spatially resolved transcriptomic studies.
SPAtest
SPAtest is an R-package to perform score test for associations between genetic variants
and binary traits using saddlepoint approximation. The methods implemented in the
package (FastSPA) can accurately calculate p-values even when the case-control ratio
is extremely unbalanced.
Reference: Kin Fai Au, Hui Jiang, Lan Lin, Yi Xing, and Wing Hung Wong. Detection of splice junctions
from paired-end RNA-seq data by SpliceMap. Nucleic Acids Research, Advance access
published on April 5, 2010.
SPOTTER
Identify regions of interest (using LD and recombination) near associated variants.
References: Yu, Y., Xia, L., Lee, S., Zhou, X., Stringham, H.M., Boehnke, M. and Mukherjee, B.,
2018. Subset-Based Analysis using Gene-Environment Interactions for Discovery of Genetic
Associations across Multiple Studies or Phenotypes. Human Heredity, 83(6), pp.283-314.
Tnseq
Identification of conditionally essential genes using high-throughput sequencing data
from transposon mutant libraries.
TRAFIC (Test for Rare-variant Association using Family-based Internal Controls) tests
for rare variant associations in affected sibpairs by comparing the allele count of
rare variants on chromosome regions shared identical by descent (IBD) to the allele
count of rare variants on non-shared chromosome regions.
References:Lin, K.H. and Zöllner, S., 2015. Robust and powerful affected sibpair test for rare
variant association. Genetic Epidemiology, 39(5), pp.325-333.
TreeLD
Infer ancestry of genomic region and analyzes for signals of disease mutations.
TransMeta is an R-package to compute single SNP p-values of trans-ethnic meta-analysis
using a kernel-based random effect model. This is an early version, and we will keep
updating it. We have recently extended it to gene-based rare-variant test (Transmeta-rare).
The packages can be downloaded from the following github.
Software that verifies whether the reads in particular file match previously known
genotypes for an individual (or group of individuals), and checks whether the reads
are contaminated as a mixture of two samples.
Reference: G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis,
M. Boehnke,and H. M. Kang, Detecting and Estimating Contamination of Human DNA Samples
in Sequencing and Array-Based Genotype Data, American Journal of Human Genetics doi:10.1016/j.ajhg.2012.09.004
(volume 91 issue 5 pp.839 - 848.
VIPER
VIPER is a method that performs Variability Preserving ImPutation for Expression Recovery
in single cell RNA sequencing studies.
Reference: Noah Snyder-Mackler, William H Majoros, Michael L Yuan, Amanda O Shaver, Jacob B
Gordon, Gisela H Kopp, Stephen A Schlebusch, Jeffrey D Wall, Susan C Alberts, Sayan
Mukherjee, Xiang Zhou and Jenny Tung (2016). Efficient genome-wide sequencing and
low-coverage pedigree analysis from non-invasively collected samples. Genetics. 203:
699-714.
WINNER
WINNER 1.1 (updated Feb 2009) is a program for correcting the winner's curse effect
in genetic associations studies.
