Showing 21 of 225 results

• Software

  released

  Peak alignment — source

  Software for aligning peaks across multiple input files to generate a unified, non-overlapping peak set, with quality control and filtering based on cross-file peak reproducibility.

  Software type: aligner

• Software

  released

  dreamlet — source

  A open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster.

  Software type: other

• Software

  released

  Scanpy — source

  Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing.

• Software

  released

  scE2G — source

  A new family of classification models, scE2G, to predict enhancer-gene regulation.

  Software type: other

• Software

  released

  ArchR — source

  ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available.

  Software type: other

• Software

  released

  APEX

  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

  BetaCells cytokines T1D — source

  A custom software used for SNP selex.

  Software type: variant annotation

• Software

  released

  MPRAflow — source

  This pipeline processes sequencing data from Massively Parallel Reporter Assays (MPRA) to create count tables for candidate sequences tested in the experiment.

• Software

  released

  combined S2G strategy (cS2G) — source

  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 annotation

• Software

  released

  Single Cell ATAC Software — source

  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 caller

• Software

  released

  Association testing and fine mapping: eQTL-Catalogue/qtlmap — source

  Association testing and fine mapping: eQTL-Catalogue/qtlmap. eQTL-Catlogue/qtlmap is a bioinformatics analysis pipeline used for QTL Analysis.

  Software type: variant annotation

• Software

  released

  Genotype QC and imputation: eQTL-Catalogue/genimpute — source

  Genotype QC and imputation: eQTL-Catalogue/genimpute. Genotype imputation and quality control workflow used by the eQTL Catalogue.

  Software type: quality metric

• Software

  released

  Gene expression QC and normalisation: eQTL-Catalogue/qcnorm — source

  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 identification

• Software

  released

  RNA-seq quantification: eQTL-Catalogue/rnaseq — source

  RNA-seq quantification: eQTL-Catalogue/rnaseq. nfcore/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.

  Software type: quantification

• Software

  released

  ptools_bin — source

  A data-sanitization software allowing raw functional genomics reads to be shared while minimizing privacy leakage, enabling principled privacy-utility trade-offs.

• Software

  released

  run.neighborhoods.py — source

  ```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

  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 regions

• Software

  released

  sambamba — source

  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

  MAGeCK — source

  Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology

• Software

  released

  CisGenome — source

  An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis

• Software

  released

  E-RANGE — source

  E-RANGE is our Python package for doing RNA-seq and ChIP-seq (hence the "dual-use"), and is a descendant of the ChIPSeq mini peak finder (Johnson, 2007).