chip-seq
tools performing common ChIP-Seq data analysis tasks
Command lineScience
Not tested on a device yet. What that means
Commands in the package
bed2bed_displaybed2sgacheck_bed.plchipcenterchipcorchipextractchippartchippeakchipscorechr_replace_sga.plcompactsgacountsgaeland2sga.plfeatreplacefilter_countsfps2sga.plgff2sga.plpartit2bed.plpartit2gff.plsga2bedsga2fps.plsga2gff.plsga2wig
About chip-seq
From Debian's package description
The ChIP-Seq software provides a set of tools performing common genome- wide ChIP- seq analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. These tools exist as stand-alone C programs and perform the following tasks:
1. Positional correlation analysis and generation of an aggregation plot (AP) (chipcor), 2. Extraction of specific genome annotation features around reference anchor points (chipextract), 3. Read centering or shifting (chipcenter), 4. Narrow peak caller using a fixed width peak size (chippeak), 5. Broad peak caller used for large regions of enrichment (chippart), 6. Feature selection tool based on a read count threshold (chipscore).
Because the ChIP-Seq tools are primarily optimized for speed, they use their own compact format for ChIP-seq data representation called SGA (Simplified Genome Annotation). SGA is a line-oriented, tab-delimited plain text format.
From Debian's description of the chip-seq package, under that package's license.
Dependencies
Depends on
libc6chip-seq-datalibmath-round-perl
Related apps
ParaViewData analysis and visualization- lokiMCMC linkage analysis on general pedigreesCommand line
GNU PSPPGNU PSPP is a program for statistical analysis of sampled data
LabPlotInteractive Data Visualization and Analysis- wekaMachine learning algorithms for data mining tasks
GraDS - Grid Analysis and Display SystemWeather data analysis and visualization
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the chip-seq package, under that package's license.
- Description: Debian's description of the chip-seq package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.