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inst/www/helpfiles/exclude_region.md
In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App
Exclude regions / features from analysis
If your samples contain known amplified / deleted regions, you might want to
exclude the amplified / deleted regions by uploading a BED file of those regions
in order to remove bias from the analysis.
If your count matrices contains genomic coordinates (peaks or regions), upload
a tab-seperated '.bed' file under the format:
chr1 880001 901000
chr1 913001 944000
chr1 959001 961000
...
Else if you want to remove specific genes / enhancers, provide a text file of
one feature name per line:
CNR2
PNRC2
SRSF10
...
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ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.
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Exclude regions / features from analysis
If your samples contain known amplified / deleted regions, you might want to exclude the amplified / deleted regions by uploading a BED file of those regions in order to remove bias from the analysis. If your count matrices contains genomic coordinates (peaks or regions), upload a tab-seperated '.bed' file under the format:
chr1 880001 901000
chr1 913001 944000
chr1 959001 961000
...
Else if you want to remove specific genes / enhancers, provide a text file of one feature name per line:
CNR2
PNRC2
SRSF10
...
Try the ChromSCape package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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