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https://www.hsph.harvard.edu/skat/
Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software)
Proper citation: SKAT (RRID:SCR_009396) Copy
http://www.helsinki.fi/~tsjuntun/multidiseq/
A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software)
Proper citation: MULTIDISEQ (RRID:SCR_009304) Copy
http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm
A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software)
Proper citation: MPDA (RRID:SCR_009303) Copy
http://bioinformatics.org/simped/
Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software)
Proper citation: SIMPED (RRID:SCR_009388) Copy
http://dmpi.duke.edu/siblink-v-30
Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software)
Proper citation: SIBLINK (RRID:SCR_009381) Copy
http://bioen-compbio.bioen.illinois.edu/FusionHunter/
Software for identifying fusion transcripts using paired-end RNA-seq.
Proper citation: FusionHunter (RRID:SCR_011895) Copy
https://gitlab.com/kyrgyzov/lsa_slurm
Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics.
Proper citation: lsa_slurm (RRID:SCR_018134) Copy
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