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ad_finemap

Code supporting analyses in paper on fine-mapping AD loci

autogenescan

Automated CAG calling pipeline for genescan data

cdna_cupcake-iso-seq

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

cellnet

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

codex2

Full-spectrum copy number variation detection by high-throughput DNA sequencing

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

datasciencecoursera

datasharing

The Leek group guide to data sharing

devnet

The DevNet project on github stores the PacBio DevNet website.

drug-seq

DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipeline

exdata_plotting1

Plotting Assignment 1 for Exploratory Data Analysis

hic-pipeline

HiC uniform processing pipeline

isoseq

monet

MONET : MOdularising NEtwork Toolbox - https://doi.org/10.1093/bioinformatics/btaa236

nono_figures_code

pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

pisces-1

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

r2-d2-model

R2-D2 model: a statistical method to identify the potential regulatory genetic variants to a gene

rnaseqeval

A tool for evaluating RNA seq mapping

snaptron

fast webservices based query tool for large sets of genomic features

sqanti3

Tool for the Quality Control of Long-Read Defined Transcriptomes

tabula-muris

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.

talon

Technology agnostic long read analysis pipeline for transcriptomes

tampor

Tunable Approach for Median Polish of Ratio -- Biological Abundance Batch Effect Removal

testing

wdl

Workflow Description Language - Specification and Implementations

whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level