deeptools

Version:: 3.5.1
Category:: bio
Cluster:: Loki

Author / Distributor

https://deeptools.readthedocs.io/

Description

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

Documentation

usage: deeptools [-h] [--version]

deepTools is a suite of python tools particularly developed for the efficient analysis of
high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.

Each tool should be called by its own name as in the following example:

$ bamCoverage -b reads.bam -o coverage.bw

If you find deepTools useful for your research please cite as:

Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert,
Andreas S. Richter, Steffen Heyne, Friederike Dündar,
and Thomas Manke. 2016. "deepTools2: A next Generation Web Server for Deep-Sequencing
Data Analysis." Nucleic Acids Research, April. doi:10.1093/nar/gkw257.

[ Tools for BAM and bigWig file processing ]
   multiBamSummary         compute read coverages over bam files. Output used for plotCorrelation or plotPCA
   multiBigwigSummary      extract scores from bigwig files. Output used for plotCorrelation or plotPCA
   correctGCBias           corrects GC bias from bam file. Don't use it with ChIP data
   bamCoverage             computes read coverage per bins or regions
   bamCompare              computes log2 ratio and other operations of read coverage of two samples per bins or regions
   bigwigCompare           computes log2 ratio and other operations from bigwig scores of two samples per bins or regions
   computeMatrix           prepares the data from bigwig scores for plotting with plotHeatmap or plotProfile
   alignmentSieve          filters BAM alignments according to specified parameters, optionally producing a BEDPE file

[ Tools for QC ]
   plotCorrelation         plots heatmaps or scatterplots of data correlation
   plotPCA                 plots PCA
   plotFingerprint         plots the distribution of enriched regions
   bamPEFragmentSize       returns the read length and paired-end distance from a bam file
   computeGCBias           computes and plots the GC bias of a sample
   plotCoverage            plots a histogram of read coverage
   estimateReadFiltering   estimates the number of reads that will be filtered from a BAM file or files given certain criteria

[Heatmaps and summary plots]
   plotHeatmap             plots one or multiple heatmaps of user selected regions over different genomic scores
   plotProfile             plots the average profile of user selected regions over different genomic scores
   plotEnrichment          plots the read/fragment coverage of one or more sets of regions

[Miscellaneous]
   computeMatrixOperations Modifies the output of computeMatrix in a variety of ways.

For more information visit: http://deeptools.readthedocs.org

optional arguments:
 -h, --help  show this help message and exit
 --version   show program's version number and exit

Examples/Usage

List available modules:
```
$ module avail deeptools
```

Load the deeptools module:

$ module load  bio/deepTools/3.5.1-foss-2021b

Check the loaded modules:
```
$ module list
```

Unload the deeptools module:

$ module unload  bio/deepTools/3.5.1-foss-2021b

Installation

Source code is obtained from Deeptools