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assign-evan

ASSIGN is an R package for adaptive profiling of genomic signatures

assign_examples

Example scripts for running the ASSIGN package on RNA-seq data

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

batchqc

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.

bedtools

A powerful toolset for genome arithmetic.

bild_signatures

celda

Bayesian Hierarchical Modeling for Clustering Single Cell RNA-Seq Data

dfjenkins3.github.io

Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll

gfrn_signatures

mpbc_genomics_paper

Code for MpBC Genomics Paper

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

ref_diff

Pipeline to compare reference genome versions through differential expression

rpackages

R package development - the Leek group way!

sctk_docs

Documentation Source for singleCellTK

shiny_kmeans_tutorial

Reproduce the k-means shiny example with step-by-step examples.

simple_sv_annotation

Simplify snpEff annotations for interesting cases

singlecelltk

sva-devel

tempassign

temp assign to fix duplicate commits

visualase

Documentation for tool to visualize allele specific expression patterns across multiple samples