Genetics Tools

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

Program that reports identical fusion genes based on gene-name annotations.

Test for association in genome-wide association studies (GWAS) using a standard linear mixed model to account for population stratification and sample structure. It calculates exact Wald or likelihood ratio test statistics and p-values, and is computationally efficient for large GWAS.

Tool for single-species active module discovery.

Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

Calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Variant tool set that discovers short variants from Next Generation Sequencing data.

BAM Statistics, Feature Counting and Annotation

BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.

A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

Data analysis, linear models and differential expression for microarray data.