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afc

Calculates allelic Fold Change (aFC) using standard input files for fastQTL.

afcn

afcs

Contains GTEX aFC estimates

allelecounter

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

aneva

ANalysis of Expression VAriance

aneva-dot

Tests Allelic Expression data for extreme imbalance w.r.t. population

aneva-dot_reference_datasets

ANEVA-DOT reference datasets

bin_scripts

Useful scripts to have in your "~/bin/" directory.

bln

An R implementation of the Binomial-Logit-Normal distribution

blnm

Tools for sampling and parameter inference of the binomial-logit-normal distribution.

bmix

BMix is a novel probabilistic method based on a constrained three-component mixture, which identifies high confidence T-to-C substitutions in PAR-CLIP data, and, based on these, reports putative RNA-protein cross-link sites.

datasets

Our old repo for storing our datasets

gene_expr_pred

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

haptwas

Haplotype Aware TWAS project

jupyter-slack-notify

A magic command for notifications via slack

pantry

pejlab.github.io

Website for the PejLab

pejtools

These are a bunch of codes that makes daily data science/bioinformatics tasks easier in Matlab. No rocket science

phaser

phasing and Allele Specific Expression from RNA-seq

recnw

Fast recursive pairwise aligner for targeted sequencing

synnet

Toolbox for design and optimization of miRNA-based synthetic classifier pathways

timex

Bioconductor package for finding mutually exclusive groups of alterations in large cancer datasets

vgdat

Utilities and starter code to match Ensembl IDs with population variance estimates from GTEx v7.