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Home Page: https://bioconductor.org/packages/ALPS
License: Other
AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project
Home Page: https://bioconductor.org/packages/ALPS
License: Other
When installing, I have the following errors and failed.
Error in unpackPkgZip(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib, libs_only, :
ERROR: failed to lock directory ‘D:\swRJ\R-3.6.1\R-3.6.1\library’ for modifying
Try removing ‘D:\swRJ\R-3.6.1\R-3.6.1\library/00LOCK’
此外: Warning message:
package ‘ALPS’ is not available (for R version 3.6.1)
multiBigwig_summary - include peaks_df
argument. Which can compute enrichments at peaks provided externally (this ignore the bed_path
from sample table)
plot_saturation_curve
get_motif_enrichments - perform de novo/known motif enrichments for a given set of peaks. Further filter by peak strength of motif enrichment signal to output good quality results
correlate_enhancer_gene - epigenomics signal vs gene expression to associate open-chromatin regions with genes
Integrate diffBind? Requires BAM file paths in sample_table. But all downstream processes will be very easy in ALPS once diffBind spits out the results.
enrichTF/TFBStools - for TF enrichment analysis
enhancer associated regulatory networks: https://github.com/bhklab/CREAM & https://genome.cshlp.org/content/early/2019/09/18/gr.248658.119
profile plots of regions - extract line plots from enrichedHeatmap. Options should be group level, sample level
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