Software type
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Showing 25 of 220 results
Software
released
APEX is a toolkit for analysis of molecular quantitative trait loci (xQTLs), such as mRNA expression or methylation levels. It performs cis and trans analysis, single- or multiple-variant analysis, and single-study or meta-analysis.Software
released
A custom software used for SNP selex.Software type: variant annotationSoftware
released
Codes to replicate the results and Figures of "Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity".Software type: variant annotationSoftware
released
Cell Ranger ATAC and Loupe Browser are software applications for analyzing and visualizing Single Cell ATAC data produced by the 10x Genomics Chromium platform.Software type: peak callerSoftware
released
Association testing and fine mapping: eQTL-Catalogue/qtlmap. eQTL-Catlogue/qtlmap is a bioinformatics analysis pipeline used for QTL Analysis.Software type: variant annotationSoftware
released
Genotype QC and imputation: eQTL-Catalogue/genimpute. Genotype imputation and quality control workflow used by the eQTL Catalogue.Software type: quality metricSoftware
released
Gene expression QC and normalisation: eQTL-Catalogue/qcnorm. This pipeline will run QC measures of both genotype and phenotype data and will normalise quantified phenotypes.Software type: transcript identificationSoftware
released
RNA-seq quantification: eQTL-Catalogue/rnaseq. nfcore/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.Software type: quantificationSoftware
released
A data-sanitization software allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs.Software
released
Perform filtering strategies to prepare prediction files for downstream variant overlap analysisSoftware
released
```run.neighborhoods.py``` will count DNase-seq (or ATAC-seq) and H3K27ac ChIP-seq reads in candidate enhancer regions. It also makes GeneList.txt, which counts reads in gene bodies and promoter regions. Replicate epigenetic experiments should be included as comma delimited list of files. Read counts in replicate experiments will be averaged when computing enhancer Activity.Software
released
makeCandidateRegions.py will take as input the narrowPeak file produced by MACS2 and then perform the following processing steps: 1. Count DNase-seq reads in each peak and retain the top N peaks with the most read counts 2. Resize each of these N peaks to be a fixed number of base pairs centered on the peak summit 3. Remove any regions listed in the 'blocklist' and include any regions listed in the 'includelist' 4. Merge any overlapping regionsSoftware
released
Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Because of its efficiency is an important work horse running in many sequencing centres around the world today.Software
released
EMMAX is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.Software
released
software for Bayesian IMputation-Based Association Mapping The program BIMBAM implements methods for assocation mapping, based on those described in Servin, B and Stephens, M (2007). Imputation-based analysis of association studies: candidate genes and quantitative traits. PLoS Genetics, 2007. BIMBAM can handle both large association studies (e.g., genome scans) and smaller studies of candidate genes/regions.