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amd

An Automated Motif Discovery Tool

aml-invivo-crispr

In vivo genome-wide CRISPR screening in murine acute myeloid leukemia

clipper

A p-value-free method for controlling false discovery rates in high-throughput biological data with two conditions

dit

Python package for information theory.

epee

Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data.

iab2

An Introduction to Applied Bioinformatics, 2nd Edition

impact-pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

jiantaoshi.github.io

lscc

Genomic landscape of somatic noncoding mutations in LSCC

lungmr

Master regulators in LUAD

mhaptk

mhaptools

monod2

MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data

moranprocess

Characterizing cancer initiation by Moran Process

mtres

netgpa

Network-based gene prioritization analysis

netora

Network-based pathway over-representation analysis

regulatoryactivities

ril-seq-interacting-regions

A simple tool to calculate accurate genome interacting regions based on RIL-seq

scage

Profiling epigenetic age in single cells

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

tramhap

TRAmHap is a novel deep-learning framework, which predicts transcriptional activity using characteristics of DNA methylation haplotypes in proximal promoters and enhancers as far as 25 kb away from TSS.