Showing 17 of 212 results

• 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

  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

  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

  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

  getVariantOverlap.py — source

  Perform filtering strategies to prepare prediction files for downstream variant overlap analysis

• Software

  released

  predict.py — source

  Compute ABC score

• 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

  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).

• Software

  released

  EMMAX — source

  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

  unknown

  Undefined software.