Allows detection and analysis of circular extrachromosomal DNA (ECDNA). ECdetect is an image analysis software package that provides a method for quantifying ECDNA from DAPI-stained metaphases in an unbiased, semi-automated fashion.
Provides a web app designed for the prediction of eukaryotic selenocysteine insertion sequence (SECIS) elements and selenoprotein genes. Selenoprotein prediction server offers 2 modules: (i) SECISearch3, a method based on the Infernal suite (INFERence of RNA ALignment) that has at its core a manually curated alignment of more than a thousand eukaryotic SECIS elements and (ii) Seblastian, a pipeline to predict selenoprotein genes in nucleotide sequences which employs the identification of SECIS elements.
Predicts BRCA1/BRCA2 deficiency in cancer. HRDetect is a whole genome sequencing (WGS)-based predictor for detection of homologous recombination (HR)-deficient tumors. The model was assessed using independent cohorts of breast, ovarian and pancreatic cancers. It was applied to a cohort of 560 breast cancer patients with 22 known germline BRCA1/BRCA2 mutation carriers and identified an additional 22 somatic BRCA1/BRCA2 null tumours and 47 tumours with functional BRCA1/BRCA2-deficiency where no mutation was detected.
Incorporates information on gene regulation from a set of markers, increases the power to detect associations relative to traditional SNP-based GWAS and known gene-based tests under a broad range of genetic architectures and provides mechanistic insights and more easily interpreted direction of effect into the observed associations. PrediXcan can detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations.
Permits ‘genecentric’ annotation of the human genome for laboratory and analytical work carried out at the Core Genotyping Facility (CGF) of the National Cancer Institute. Genewindow integrates data available in the public databases with internal annotations from sequence data generated by our laboratory. It is configured for the human genome and can be applied to other genomes and integrated with the analysis, storage and archiving of data generated in any laboratory setting.
Permits to evaluate pleiotropy in a standard mendelian randomization (MR) model. MR-PRESSO contains three main functions: (1) detection of pleiotropy (MR-PRESSO global test); 2) correction of pleiotropy via outlier removal (MR-PRESSO outlier test); and 3) testing of significant differences in the causal estimates before and after correction for outliers (MR-PRESSO distortion test). The tool is flexible and can be used in several different MR tests.
Characterizes the orientation of individual duplicons for a given primate genomic sequence. DupMasker fixes the fine mosaic substructure for a given complex duplication block. It gathers data about the ancestral origin of a major part of human segmental duplications. This tool is able to construct annotation of the duplication composition of sequenced clones. It starts by screening sequences for all common interspersed repeats.
A mixed-model approach that enables joint analysis across multiple correlated traits while accounting for population structure and relatedness. mtSet effectively combines the benefits of set tests with multi-trait modeling and is computationally efficient, enabling genetic analysis of large cohorts (up to 500,000 individuals) and multiple traits.
Consists in a benchmark dataset. Syndip has been designed from high-quality PacBio assemblies of two independent, homozygous cell lines. It can provide an estimation of the error rate of small variant calls in a realistic context. It leverages the power of long-read sequencing technologies while avoiding the difficulties in calling heterozygotes from relatively noisy data. Moreover, it doesn’t depend on short-read data and short-read variant callers.
Allows user to handle files recorded under the GCTx format, which is especially suited to manage data matrices paired accompanied by metadata annotations. cmap gathers an assortment of open source software, available in four different languages, providing the ability to interact with the features supplied by the Connectivity map resources. These programs aim to ease their integration in existing frameworks.
Integrates quantitative trait loci (QTL) information with genome wide association studies (GWAS) results to map disease-associated genes. MetaXcan was trained on transcriptome models in 44 human tissues from Genotype-Tissue Expression (GTEx) and was able to estimate their effect on phenotypes from over available genome-wide association meta-analysis (GWAMA) studies. It uses single nucleotide polymorphism (SNP)-level association results.
Allows users to generate sliding window plots of seven different sequence properties. ASEQH is intended for analysis of prokaryotic genomes but it can be applied to eukaryotic chromosomes with some limitations. Percentage of G and C nucleotides in the sliding window is plotted with respect to the position of the center of the window. The G+C percentage is calculated for all genes with their mid-point within the window.
Identifies gene-by-gene and gene-by-environment interactions. GMDR allows users to perform analyses for detection of multifactor interactions with large-scale data. The software implements a set of methods on the analysis of interactions with diverse study designs such as case-control design, family based design or a combination of both. GMDR also provides features such as large-scale data management and preprocessing. It can assist in revealing genetic architecture in terms of gene-gene interactions underlying complex traits.
Offers a solution to explore the problematic topic of genomic data sharing. DNAdigest enables efficient and ethical data sharing. It aims to engage the research community in discussions about the problems and potential solutions, and to build tools to incentivize and increase data access and reuse in genomics research. The platform gives access to raw genomic data in order to validate research hypotheses.
Reassembles position weight matrix (PWMs) from sequence logo images with the aim of helping in the study of transcription factor (TF)-DNA interaction. Logo2PWN is available via a web application or a standalone software. It converts the image file to a common three-channel RGB formatted file, and automatically re-generates the sequence logo for the estimated PWM using enologos.
Provides a comprehensive selection of methods for the identification of important transcriptional regulators. The web service of RegulatorTrail can be used in four distinct application scenarios to either analyse gene lists, gene expression data or epigenetic data. It detects meaningful regulators that might explain the increased malignancy of metastatic melanoma compared to primary tumors as well as important regulators in macrophages.
Searches for conserved splice sites around peaks of local sequence similarity in order to identify candidate exons from which complete gene models are then constructed. AGenDA is a homology-based gene-finding program. The program takes a DIALIGN alignment of two genomic sequences as input. It is possible to apply comparative gene-finding approaches to different species at varying evolutionary distances.
Rapid and accurate detection of antibiotic resistance in pathogens is an urgent need, affecting both patient care and population-scale control. Mykrobe predictor is a generic framework extensible to many species which can identify species, resistance profile and other genomic features such as virulence elements and phylogenetic lineage, within 3 minutes on a standard laptop.
Assists in the elucidation of differences in gene structure between individuals of a species. ACE detects possible functional changes in gene structure that may result from sequence variants. The software can identify changes to gene structure that may alter the function of the resulting protein, even if that protein is highly conserved between species. It is applicable to nonhuman species (other model and non-model animal or plant species). ACE includes the splice graph random field (SGRF) model for variant-aware gene structure prediction.