lijiacd985 Goto Github PK

3dchromatin_replicateqc

Software to compute reproducibility and quality scores for Hi-C data

analysis_shogun

Analysis scripts and code for reproducing the analysis for the SHOGUN paper

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

awesome-single-cell

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

bioinfo-combio

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

biomarker-identification

This repository is the author implementation of the paper "Biomarker Identification by Reversing the Learning Mechanism of Autoencoder and Recursive Feature Elimination"

bis-tools

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )

biscuit

BISulfite-seq CUI Toolkit

bwa-meth

fast and accurate alignment of BS-Seq reads

camelia

imputation in single-cell methylomes

cfchip-seek

cell-free ChIP-seq pipeline

cfchip-seq

Code to accompany publication on cell free chromatin immunoprecipitation (cfChIP)

cfchip_manuscript

cooler

A cool place to store your Hi-C

cpg-transformer

CpG Transformer for imputation of single-cell methylomes

episcanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

granulator

hamip

HaMiP: DNA hydroxymethylation analysis of Cytosine-5-methylenesulfonate ImmunoPrecipitation sequencing

hic-spector

Spectral and reproducibility analysis of Hi-C contact maps

hic_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

hic_tools

A collection of tools for Hi-C data analysis

hicpipe

an efficient Hi-C data processing pipeline

inspectro

Hi-C spectral analysis workflow

meth_atlas

mmint

Versatile integrative analysis of DNA methylation, ChIP-seq and RNAseq

mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

rima

scvelo

RNA Velocity generalized through dynamical modeling

seacr

SEACR: Sparse Enrichment Analysis for CUT&RUN

seurat.utils

Various utility functions for Seurat v3