MAnorm
Introduction
ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed.
Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.
Citation
Documentation
To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io
Installation
The latest release of MAnorm is available at PyPI:
$ pip install manorm
Or you can install MAnorm via conda:
$ conda install -c bioconda manorm
Galaxy Installation
MAnorm is also available on Galaxy, you can incorporate MAnorm into your own Galaxy instance.
Please search and install MAnorm via the Galaxy Tool Shed.
Basic Usage
$ manorm --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed --n1 name1 --n2 name2 -o output_dir
Note: Using -h/–help for the details of all arguments.
License
1 maintainer
Metadata
1 maintainer
Release files for MAnorm 1.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| MAnorm-1.3.0.tar.gz | 4.7 MB | Details |
Release files / MAnorm-1.3.0.tar.gz
| Download URL | MAnorm-1.3.0.tar.gz |
|---|---|
| Size | 4.7 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.0.0.post20200309 requests-toolbelt/0.9.1 tqdm/4.44.1 CPython/3.7.6
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