ALLCools: ALL methyl-Cytosine tools

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Installation
Input Files
Analysis Steps
Examples In This Document

CELLULAR ANALYSIS

Basic Clustering Walk-through
- Basic Cell Clustering Using 100Kb Bins
- Basic Cell Clustering Using mCG-5Kb Bins
Step-by-step Clustering Analysis
- Step-by-step Clustering Using 100Kb bins
- Step-by-step Clustering using mCG-5Kb Input
Differential Methylated Genes Analysis
Data Integration
Doublets Identification
- Calculate Cell Doublet Score

GENOMIC ANALYSIS

Post-clustering Genomic Analysis
Motif Scan and Analysis
- Motif Scan
- Motif Enrichment Analysis
Region-Region Correlation Analysis
- Prepare Cluster-by-Gene mC Profile
- DMR-Gene Correlation
REPTILE
- Prepare REPTILE
- Predict Enhancer with REPTILE Algorithm

COMMAND LINE TOOLS

Entry Point
allcools allc
allcools standard
allcools profile
allcools tbi
allcools merge
allcools extract
allcools bw
allcools region
allcools generate-dataset
allcools mcds
allcools mcad
allcools table-to-allc

API

ALLCools

PROJECT INFO

Citation And Reference
Changelog

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Contents

Submodules

ALLCools.sandbox.igv

Contents

Submodules

`ALLCools.sandbox.igv`¶

Submodules¶

ALLCools.sandbox.igv.BaseClass
ALLCools.sandbox.igv.Session
ALLCools.sandbox.igv.Track
ALLCools.sandbox.igv.defaults
ALLCools.sandbox.igv.make_session

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ALLCools.sandbox

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ALLCools.sandbox.igv.BaseClass

By Hanqing Liu
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