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bioc
plotgardener:Coordinate-Based Genomic Visualization Package for R
Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
Maintained by Nicole Kramer. Last updated 5 months ago.
visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhiccpp
309 stars 10.17 score 167 scripts 3 dependentsbioc
HMMcopy:Copy number prediction with correction for GC and mappability bias for HTS data
Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.
Maintained by Daniel Lai. Last updated 5 months ago.
sequencingpreprocessingvisualizationcopynumbervariationmicroarray
5.89 score 129 scripts 1 dependents
wilarhen
measuRing:Detection and Control of Tree-Ring Widths on Scanned Image Sections
Identification of ring borders on scanned image sections from dendrochronological samples. Processing of image reflectances to produce gray matrices and time series of smoothed gray values. Luminance data is plotted on segmented images for users to perform both: visual identification of ring borders or control of automatic detection. Routines to visually include/exclude ring borders on the R graphical devices, or automatically detect ring borders using a linear detection algorithm. This algorithm detects ring borders according to positive/negative extreme values in the smoothed time-series of gray values. Most of the in-package routines can be recursively implemented using the multiDetect() function.
Maintained by Wilson Lara. Last updated 5 days ago.
1.80 score 21 scripts 1 dependents