liulab-dfci Goto Github PK

bioinfo-combio

The rendered book can be found at https://liulab-dfci.github.io/bioinfo-combio/

chips

A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data

chromap

Fast alignment and preprocessing of chromatin profiles

cop1_cell_2021

Code for "In vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target"

deepbcr

Deep learning framework for cancer-type classification and binding affinity estimation using B cell receptor repertoires

deepdegron

Deep learning model to predict degron sequences

degradability2021

Protein-intrinsic features predict tractability of targeted protein degradation

drugcellnet

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model

lisa

epigenome analysis to rank transcription factors

lisa2

liulab-dfci.github.io

Know more about Shirley Liu lab at

macs

MACS -- Model-based Analysis of ChIP-Seq

maestro

Single-cell Transcriptome and Regulome Analysis Pipeline

mageck

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

mageckflute

Integrative analysis pipeline for pooled CRISPR functional genetic screens

mapd

Model-based Analysis of Protein Degradability

mat

Model-based Analysis of Tiling-array (MAT): A model-based algorithm for finding enriched regions in ChIP-Chip experiments.

rima

rima_pipeline

tidepy

TIDE (Tumor Immune Dysfunction and Exclusion), a gene expression biomarker to predict the clinical response to immune checkpoint blockade in Python.

trust4

TCR and BCR assembly from RNA-seq data

trust4_analysis

trust4_manuscript_evaluation

TRUST4 manuscript evaluation

visualizirr