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bioc
Gviz:Plotting data and annotation information along genomic coordinates
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.
Maintained by Robert Ivanek. Last updated 5 months ago.
visualizationmicroarraysequencing
79 stars 13.05 score 1.4k scripts 46 dependents
henrikbengtsson
PSCBS:Analysis of Parent-Specific DNA Copy Numbers
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
Maintained by Henrik Bengtsson. Last updated 1 years ago.
acghcopynumbervariantssnpmicroarrayonechanneltwochannelgenetics
7 stars 7.63 score 34 scripts 9 dependentshenrikbengtsson
aroma.core:Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Maintained by Henrik Bengtsson. Last updated 2 years ago.
microarrayonechanneltwochannelmultichanneldataimportdatarepresentationguivisualizationpreprocessingqualitycontrolacghcopynumbervariants
1 stars 4.30 score 16 scripts 6 dependentsbioc
GUIDEseq:GUIDE-seq and PEtag-seq analysis pipeline
The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.
Maintained by Lihua Julie Zhu. Last updated 5 months ago.
immunooncologygeneregulationsequencingworkflowstepcrispr
4.23 score 14 scripts